EDIT

/**

* Copyright (C) 2008 EDIT

* European Distributed Institute of Taxonomy

* http://www.e-taxonomy.eu

*/

package eu.etaxonomy.cdm.persistence.dao.hibernate.occurrence;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

import java.util.HashSet;

import java.util.List;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.hibernate.Criteria;

import org.hibernate.Hibernate;

import org.hibernate.Query;

import org.hibernate.Session;

import org.hibernate.criterion.Disjunction;

import org.hibernate.criterion.ProjectionList;

import org.hibernate.criterion.Projections;

import org.hibernate.criterion.Restrictions;

import org.hibernate.envers.query.AuditEntity;

import org.hibernate.envers.query.AuditQuery;

import org.hibernate.search.FullTextSession;

import org.hibernate.search.Search;

import org.springframework.beans.factory.annotation.Autowired;

import org.springframework.stereotype.Repository;

import eu.etaxonomy.cdm.model.common.CdmBase;

import eu.etaxonomy.cdm.model.description.DescriptionBase;

import eu.etaxonomy.cdm.model.description.IndividualsAssociation;

import eu.etaxonomy.cdm.model.location.Point;

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.molecular.DnaSample;

import eu.etaxonomy.cdm.model.name.HomotypicalGroup;

import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;

import eu.etaxonomy.cdm.model.occurrence.FieldUnit;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;

import eu.etaxonomy.cdm.model.taxon.Synonym;

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonBase;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

import eu.etaxonomy.cdm.model.view.AuditEvent;

import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;

import eu.etaxonomy.cdm.persistence.dao.hibernate.common.IdentifiableDaoBase;

import eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl;

import eu.etaxonomy.cdm.persistence.dao.name.IHomotypicalGroupDao;

import eu.etaxonomy.cdm.persistence.dao.name.ITaxonNameDao;

import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;

import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;

import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

import eu.etaxonomy.cdm.persistence.query.OrderHint;

/**

 * @author a.babadshanjan

 * @since 01.09.2008

 */

@Repository

public class OccurrenceDaoHibernateImpl

          extends IdentifiableDaoBase<SpecimenOrObservationBase>

          implements IOccurrenceDao {

    @SuppressWarnings("unused")

    private static final Logger logger = Logger.getLogger(TaxonDaoHibernateImpl.class);

    @Autowired

    private IDescriptionDao descriptionDao;

    @Autowired

    private ITaxonNameDao taxonNameDao;

    @Autowired

    private IHomotypicalGroupDao homotypicalGroupDao;

    public OccurrenceDaoHibernateImpl() {

        super(SpecimenOrObservationBase.class);

        indexedClasses = new Class[7];

        indexedClasses[0] = FieldUnit.class;

        indexedClasses[1] = DerivedUnit.class;

        indexedClasses[5] = DnaSample.class;

    }

    @Override

    public long countDerivationEvents(SpecimenOrObservationBase occurence) {

        checkNotInPriorView("OccurrenceDaoHibernateImpl.countDerivationEvents(SpecimenOrObservationBase occurence)");

        Query query = getSession().createQuery("select count(distinct derivationEvent) from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");

        query.setParameter("occurence", occurence);

        return (Long)query.uniqueResult();

    }

    @Override

    public long countDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase) {

        AuditEvent auditEvent = getAuditEventFromContext();

        if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {

            Criteria criteria = getCriteria(DeterminationEvent.class);

            if(occurrence != null) {

                criteria.add(Restrictions.eq("identifiedUnit",occurrence));

            }

            if(taxonBase != null) {

                criteria.add(Restrictions.eq("taxon",taxonBase));

            }

            criteria.setProjection(Projections.rowCount());

            return (Long)criteria.uniqueResult();

        } else {

            AuditQuery query = makeAuditQuery(DeterminationEvent.class,auditEvent);

            if(occurrence != null) {

                query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));

            }

            if(taxonBase != null) {

                query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));

            }

            query.addProjection(AuditEntity.id().count());

            return (Long)query.getSingleResult();

        }

    }

    @Override

    public long countMedia(SpecimenOrObservationBase occurence) {

        checkNotInPriorView("OccurrenceDaoHibernateImpl.countMedia(SpecimenOrObservationBase occurence)");

        Query query = getSession().createQuery("select count(media) from SpecimenOrObservationBase occurence join occurence.media media where occurence = :occurence");

        query.setParameter("occurence", occurence);

        return (Long)query.uniqueResult();

    }

    @Override

    public List<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {

        checkNotInPriorView("OccurrenceDaoHibernateImpl.getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber)");

        Query query = getSession().createQuery("select distinct derivationEvent from DerivationEvent derivationEvent join derivationEvent.originals occurence where occurence = :occurence");

        query.setParameter("occurence", occurence);

        addPageSizeAndNumber(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<DerivationEvent> result = query.list();

        defaultBeanInitializer.initializeAll(result, propertyPaths);

        return result;

    }

    @Override

    public List<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {

        AuditEvent auditEvent = getAuditEventFromContext();

        if(auditEvent.equals(AuditEvent.CURRENT_VIEW)) {

            Criteria criteria = getSession().createCriteria(DeterminationEvent.class);

            if(occurrence != null) {

                criteria.add(Restrictions.eq("identifiedUnit",occurrence));

            }

            if(taxonBase != null) {

                criteria.add(Restrictions.eq("taxon",taxonBase));

            }

            addPageSizeAndNumber(criteria, pageSize, pageNumber);

            @SuppressWarnings("unchecked")

            List<DeterminationEvent> result = criteria.list();

            defaultBeanInitializer.initializeAll(result, propertyPaths);

            return result;

        } else {

            AuditQuery query = getAuditReader().createQuery().forEntitiesAtRevision(DeterminationEvent.class,auditEvent.getRevisionNumber());

            if(occurrence != null) {

                query.add(AuditEntity.relatedId("identifiedUnit").eq(occurrence.getId()));

            }

            if(taxonBase != null) {

                query.add(AuditEntity.relatedId("taxon").eq(taxonBase.getId()));

            }

            addPageSizeAndNumber(query, pageSize, pageNumber);

            @SuppressWarnings("unchecked")

            List<DeterminationEvent> result = query.getResultList();

            defaultBeanInitializer.initializeAll(result, propertyPaths);

            return result;

        }

    }

    @Override

    public List<Media> getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths) {

        checkNotInPriorView("OccurrenceDaoHibernateImpl.getMedia(SpecimenOrObservationBase occurence, Integer pageSize, Integer pageNumber, List<String> propertyPaths)");

        Query query = getSession().createQuery(

                "   SELECT media "

                + " FROM SpecimenOrObservationBase occurence "

                + " JOIN occurence.media media "

                + " WHERE occurence = :occurence");

        query.setParameter("occurence", occurence);

        addPageSizeAndNumber(query, pageSize, pageNumber);

        @SuppressWarnings("unchecked")

        List<Media> results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public void rebuildIndex() {

        FullTextSession fullTextSession = Search.getFullTextSession(getSession());

        for(SpecimenOrObservationBase<?> occurrence : list(null,null)) { // re-index all taxon base

            for(DeterminationEvent determination : occurrence.getDeterminations()) {

                Hibernate.initialize(determination.getActor());

                Hibernate.initialize(determination.getTaxon());

            }

            Hibernate.initialize(occurrence.getDefinition());

            if(occurrence instanceof DerivedUnit) {

                DerivedUnit derivedUnit = (DerivedUnit) occurrence;

                Hibernate.initialize(derivedUnit.getCollection());

                if(derivedUnit.getCollection() != null) {

                    Hibernate.initialize(derivedUnit.getCollection().getSuperCollection());

                    Hibernate.initialize(derivedUnit.getCollection().getInstitute());

                }

                Hibernate.initialize(derivedUnit.getStoredUnder());

                SpecimenOrObservationBase<?> original = derivedUnit.getOriginalUnit();

                if(original != null && original.isInstanceOf(FieldUnit.class)) {

                    FieldUnit fieldUnit = CdmBase.deproxy(original, FieldUnit.class);

                    Hibernate.initialize(fieldUnit.getGatheringEvent());

                    if(fieldUnit.getGatheringEvent() != null) {

                        Hibernate.initialize(fieldUnit.getGatheringEvent().getActor());

                    }

                }

            }

            fullTextSession.index(occurrence);

        }

        fullTextSession.flushToIndexes();

    }

    @Override

    public long count(Class<? extends SpecimenOrObservationBase> clazz,	TaxonName determinedAs) {

        Criteria criteria = getCriteria(clazz);

        criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));

        criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));

        return (Long)criteria.uniqueResult();

    }

    @Override

    public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs,

            Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {

        Criteria criteria = getCriteria(clazz);

        criteria.createCriteria("determinations").add(Restrictions.eq("taxonName", determinedAs));

        addPageSizeAndNumber(criteria, pageSize, pageNumber);

        addOrder(criteria,orderHints);

        @SuppressWarnings({ "unchecked", "rawtypes" })

        List<SpecimenOrObservationBase> results = criteria.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public long count(Class<? extends SpecimenOrObservationBase> clazz,	TaxonBase determinedAs) {

        Criteria criteria = getCriteria(clazz);

        criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));

        criteria.setProjection(Projections.projectionList().add(Projections.rowCount()));

        return (Long)criteria.uniqueResult();

    }

    @Override

    public List<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs,

            Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {

        Criteria criteria = getCriteria(clazz);

        criteria.createCriteria("determinations").add(Restrictions.eq("taxon", determinedAs));

        addPageSizeAndNumber(criteria, pageSize, pageNumber);

        addOrder(criteria,orderHints);

        @SuppressWarnings({ "unchecked", "rawtypes" })

        List<SpecimenOrObservationBase> results = criteria.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> findOccurrencesUuidAndTitleCache(

            Class<T> clazz, String queryString, String significantIdentifier, SpecimenOrObservationType recordBasis,

            Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, Integer limit, Integer start,

            List<OrderHint> orderHints) {

        Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,

                associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, null);

        if(criteria!=null){

            ProjectionList projectionList = Projections.projectionList();

            projectionList.add(Projections.property("uuid"));

            projectionList.add(Projections.property("id"));

            projectionList.add(Projections.property("titleCache"));

            criteria.setProjection(projectionList);

            @SuppressWarnings("unchecked")

            List<Object[]> result = criteria.list();

            List<UuidAndTitleCache<SpecimenOrObservationBase>> uuidAndTitleCacheList = new ArrayList<>();

            for(Object[] object : result){

                uuidAndTitleCacheList.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));

            }

            return uuidAndTitleCacheList;

        }else{

            return Collections.emptyList();

        }

    }

    @Override

    public <T extends SpecimenOrObservationBase> List<T> findOccurrences(Class<T> clazz, String queryString,

            String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,

            MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,

                associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);

        if(criteria!=null){

            @SuppressWarnings("unchecked")

            List<T> results = criteria.list();

            defaultBeanInitializer.initializeAll(results, propertyPaths);

            return results;

        }else{

            return Collections.emptyList();

        }

    }

    private <T extends SpecimenOrObservationBase> Criteria createFindOccurrenceCriteria(Class<T> clazz, String queryString,

            String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, Integer limit,

            Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        Criteria criteria = null;

        if(clazz == null) {

            criteria = getSession().createCriteria(type);

        } else {

            criteria = getSession().createCriteria(clazz);

        }

        //queryString

        if (queryString != null) {

            if(matchmode == null) {

                matchmode = MatchMode.ANYWHERE;

                criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString)));

            } else if(matchmode == MatchMode.BEGINNING) {

                criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.START));

            } else if(matchmode == MatchMode.END) {

                criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.END));

            } else if(matchmode == MatchMode.EXACT) {

                criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.EXACT));

            } else {

                criteria.add(Restrictions.ilike("titleCache", matchmode.queryStringFrom(queryString), org.hibernate.criterion.MatchMode.ANYWHERE));

            }

        }

        //significant identifier

        if (significantIdentifier != null) {

            criteria.add(Restrictions.or(Restrictions.ilike("accessionNumber", significantIdentifier),

                    Restrictions.ilike("catalogNumber", significantIdentifier), Restrictions.ilike("barcode", significantIdentifier)));

        }

        //recordBasis/SpecimenOrObservationType

        Set<SpecimenOrObservationType> typeAndSubtypes = new HashSet<SpecimenOrObservationType>();

        if(recordBasis==null){

            //add all types

            SpecimenOrObservationType[] values = SpecimenOrObservationType.values();

            for (SpecimenOrObservationType specimenOrObservationType : values) {

                typeAndSubtypes.add(specimenOrObservationType);

            }

        }

        else{

            typeAndSubtypes = recordBasis.getGeneralizationOf(true);

            typeAndSubtypes.add(recordBasis);

        }

        criteria.add(Restrictions.in("recordBasis", typeAndSubtypes));

        Set<UUID> associationUuids = new HashSet<UUID>();

        //taxon associations

        if(associatedTaxon!=null){

            List<UuidAndTitleCache<SpecimenOrObservationBase>> associatedTaxaList = listUuidAndTitleCacheByAssociatedTaxon(clazz, associatedTaxon, limit, start, orderHints);

            if(associatedTaxaList!=null){

                for (UuidAndTitleCache<SpecimenOrObservationBase> uuidAndTitleCache : associatedTaxaList) {

                    associationUuids.add(uuidAndTitleCache.getUuid());

                }

            }

        }

        //taxon name associations

        else if(associatedTaxonName!=null){

            List<? extends SpecimenOrObservationBase> associatedTaxaList = listByAssociatedTaxonName(clazz, associatedTaxonName, limit, start, orderHints, propertyPaths);

            if(associatedTaxaList!=null){

                for (SpecimenOrObservationBase<?> specimenOrObservationBase : associatedTaxaList) {

                    associationUuids.add(specimenOrObservationBase.getUuid());

                }

            }

        }

        if(associatedTaxon!=null || associatedTaxonName!=null){

            if(!associationUuids.isEmpty()){

                criteria.add(Restrictions.in("uuid", associationUuids));

            }

            else{

                return null;

            }

        }

        if(limit != null) {

            if(start != null) {

                criteria.setFirstResult(start);

            } else {

                criteria.setFirstResult(0);

            }

            criteria.setMaxResults(limit);

        }

        if(orderHints!=null){

            addOrder(criteria,orderHints);

        }

        return criteria;

    }

    @Override

    public <T extends SpecimenOrObservationBase> long countOccurrences(Class<T> clazz, String queryString,

            String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName,

            MatchMode matchmode, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        Criteria criteria = createFindOccurrenceCriteria(clazz, queryString, significantIdentifier, recordBasis,

                associatedTaxon, associatedTaxonName, matchmode, limit, start, orderHints, propertyPaths);

        if(criteria!=null){

            criteria.setProjection(Projections.rowCount());

            return (Long)criteria.uniqueResult();

        }else{

            return 0;

        }

    }

    @Override

    public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(Integer limit, String pattern) {

        List<UuidAndTitleCache<DerivedUnit>> list = new ArrayList<>();

        Session session = getSession();

        String hql = "SELECT uuid, id, titleCache "

                + " FROM " + type.getSimpleName()

                + " WHERE NOT dtype = " + FieldUnit.class.getSimpleName();

        Query query;

        if (pattern != null){

            pattern = pattern.replace("*", "%");

            pattern = pattern.replace("?", "_");

            pattern = pattern + "%";

            query = session.createQuery(hql +" AND titleCache like :pattern");

            query.setParameter("pattern", pattern);

        } else {

            query = session.createQuery(hql);

        }

        if (limit != null){

           query.setMaxResults(limit);

        }

        @SuppressWarnings("unchecked")

        List<Object[]> result = query.list();

        for(Object[] object : result){

            list.add(new UuidAndTitleCache<DerivedUnit>(DerivedUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));

        }

        return list;

    }

    @Override

    public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {

        List<UuidAndTitleCache<FieldUnit>> list = new ArrayList<>();

        Session session = getSession();

        Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where dtype = " + FieldUnit.class.getSimpleName());

        @SuppressWarnings("unchecked")

        List<Object[]> result = query.list();

        for(Object[] object : result){

            list.add(new UuidAndTitleCache<FieldUnit>(FieldUnit.class, (UUID) object[0], (Integer)object[1], (String) object[2]));

        }

        return list;

    }

    @Override

    public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxonName(Class<T> type,

            TaxonName associatedTaxonName, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        @SuppressWarnings("rawtypes")

        Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();

        // A Taxon name may be referenced by the DeterminationEvent of the SpecimenOrObservationBase

        @SuppressWarnings("rawtypes")

        List<SpecimenOrObservationBase> byDetermination = list(type, associatedTaxonName, null, 0, null, null);

        setOfAll.addAll(byDetermination);

        if(setOfAll.size() == 0){

            // no need querying the data base

            return new ArrayList<T>();

        }

        String queryString =

            "SELECT sob " +

            " FROM SpecimenOrObservationBase sob" +

            " WHERE sob in (:setOfAll)";

        if(type != null && !type.equals(SpecimenOrObservationBase.class)){

            queryString += " AND sob.class = :type";

        }

        queryString += orderByClause("sob", orderHints);

        Query query = getSession().createQuery(queryString);

        query.setParameterList("setOfAll", setOfAll);

        if(type != null && !type.equals(SpecimenOrObservationBase.class)){

            query.setParameter("type", type.getSimpleName());

        }

        addLimitAndStart(query, limit, start);

        @SuppressWarnings("unchecked")

        List<T> results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    private List<SpecimenNodeWrapper> querySpecimen(

            Query query, List<UUID> taxonNodeUuids,

            Integer limit, Integer start){

        query.setParameterList("taxonNodeUuids", taxonNodeUuids);

        addLimitAndStart(query, limit, start);

        List<SpecimenNodeWrapper> list = new ArrayList<>();

        @SuppressWarnings("unchecked")

        List<Object[]> result = query.list();

        for(Object[] object : result){

            list.add(new SpecimenNodeWrapper(

                    new UuidAndTitleCache<>(

                            (UUID) object[0],

                            (Integer) object[1],

                            (String) object[2]),

                    (TaxonNode)object[3]));

        }

        return list;

    }

    private List<SpecimenNodeWrapper> queryIndividualAssociatedSpecimen(List<UUID> taxonNodeUuids,

            Integer limit, Integer start){

        String queryString =  "SELECT "

                + "de.associatedSpecimenOrObservation.uuid, "

                + "de.associatedSpecimenOrObservation.id, "

                + "de.associatedSpecimenOrObservation.titleCache, "

                + "tn "

                + "FROM DescriptionElementBase AS de "

                + "LEFT JOIN de.inDescription AS d "

                + "LEFT JOIN d.taxon AS t "

                + "JOIN t.taxonNodes AS tn "

                + "WHERE d.class = 'TaxonDescription' "

                + "AND tn.uuid in (:taxonNodeUuids) "

                ;

        Query query = getSession().createQuery(queryString);

        return querySpecimen(query, taxonNodeUuids, limit, start);

    }

    private List<SpecimenNodeWrapper> queryTypeSpecimen(List<UUID> taxonNodeUuids,

            Integer limit, Integer start){

        String queryString =  "SELECT "

                + "td.typeSpecimen.uuid, "

                + "td.typeSpecimen.id, "

                + "td.typeSpecimen.titleCache, "

                + "tn "

                + "FROM SpecimenTypeDesignation AS td "

                + "LEFT JOIN td.typifiedNames AS tn "

                + "LEFT JOIN tn.taxonBases AS t "

                + "JOIN t.taxonNodes AS tn "

                + "WHERE tn.uuid in (:taxonNodeUuids) "

                ;

        Query query = getSession().createQuery(queryString);

        return querySpecimen(query, taxonNodeUuids, limit, start);

    }

    private List<SpecimenNodeWrapper> queryTaxonDeterminations(List<UUID> taxonNodeUuids,

            Integer limit, Integer start){

        String queryString =  "SELECT "

                + "det.identifiedUnit.uuid, "

                + "det.identifiedUnit.id, "

                + "det.identifiedUnit.titleCache, "

                + "tn "

                + "FROM DeterminationEvent AS det "

                + "LEFT JOIN det.taxon AS t "

                + "JOIN t.taxonNodes AS tn "

                + "WHERE tn.uuid in (:taxonNodeUuids) "

                ;

        Query query = getSession().createQuery(queryString);

        return querySpecimen(query, taxonNodeUuids, limit, start);

    }

    private List<SpecimenNodeWrapper> queryTaxonNameDeterminations(List<UUID> taxonNodeUuids,

            Integer limit, Integer start){

        String queryString =  "SELECT "

                + "det.identifiedUnit.uuid, "

                + "det.identifiedUnit.id, "

                + "det.identifiedUnit.titleCache, "

                + "tn "

                + "FROM DeterminationEvent AS det "

                + "LEFT JOIN det.taxonName AS n "

                + "LEFT JOIN n.taxonBases AS t "

                + "JOIN t.taxonNodes AS tn "

                + "WHERE tn.uuid in (:taxonNodeUuids) "

                ;

        Query query = getSession().createQuery(queryString);

        return querySpecimen(query, taxonNodeUuids, limit, start);

    }

    @Override

    public Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(List<UUID> taxonNodeUuids,

            Integer limit, Integer start){

        Collection<SpecimenNodeWrapper> wrappers = new HashSet<>();

        wrappers.addAll(queryIndividualAssociatedSpecimen(taxonNodeUuids, limit, start));

        wrappers.addAll(queryTaxonDeterminations(taxonNodeUuids, limit, start));

        wrappers.addAll(queryTaxonNameDeterminations(taxonNodeUuids, limit, start));

        wrappers.addAll(queryTypeSpecimen(taxonNodeUuids, limit, start));

        return wrappers;

    }

    @Override

    public <T extends SpecimenOrObservationBase> List<UuidAndTitleCache<SpecimenOrObservationBase>> listUuidAndTitleCacheByAssociatedTaxon(Class<T> clazz, Taxon associatedTaxon,

            Integer limit, Integer start, List<OrderHint> orderHints){

        Query query = createSpecimenQuery("sob.uuid, sob.id, sob.titleCache", clazz, associatedTaxon, limit, start, orderHints, null);

        if(query==null){

            return Collections.emptyList();

        }

        List<UuidAndTitleCache<SpecimenOrObservationBase>> list = new ArrayList<>();

        @SuppressWarnings("unchecked")

        List<Object[]> result = query.list();

        for(Object[] object : result){

            list.add(new UuidAndTitleCache<>((UUID) object[0],(Integer) object[1], (String) object[2]));

        }

        return list;

    }

    @Override

    public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> clazz,

            Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        Query query = createSpecimenQuery("sob", clazz, associatedTaxon, limit, start, orderHints, propertyPaths);

        if(query==null){

            return Collections.emptyList();

        }

        @SuppressWarnings("unchecked")

        List<T> results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    private <T extends SpecimenOrObservationBase> Query createSpecimenQuery(String select, Class<T> clazz,

            Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths){

        Set<SpecimenOrObservationBase> setOfAll = new HashSet<>();

        Set<Integer> setOfAllIds = new HashSet<>();

        Criteria criteria = null;

        if(clazz == null) {

            criteria = getSession().createCriteria(type, "specimen");

        } else {

            criteria = getSession().createCriteria(clazz, "specimen");

        }

        Disjunction determinationOr = Restrictions.disjunction();

        // A Taxon may be referenced by the DeterminationEvent of the SpecimenOrObservationBase

        Criteria determinationsCriteria = criteria.createCriteria("determinations");

        determinationOr.add(Restrictions.eq("taxon", associatedTaxon));

        //check also for synonyms

        for (Synonym synonym : associatedTaxon.getSynonyms()) {

            determinationOr.add(Restrictions.eq("taxon", synonym));

        }

        //check also for name determinations

        determinationOr.add(Restrictions.eq("taxonName", associatedTaxon.getName()));

        for (TaxonName synonymName : associatedTaxon.getSynonymNames()) {

            determinationOr.add(Restrictions.eq("taxonName", synonymName));

        }

        determinationsCriteria.add(determinationOr);

        if(limit != null) {

            if(start != null) {

                criteria.setFirstResult(start);

            } else {

                criteria.setFirstResult(0);

            }

            criteria.setMaxResults(limit);

        }

        criteria.setProjection(Projections.property("id"));

        addOrder(criteria,orderHints);

        @SuppressWarnings("unchecked")

        List<Integer> detResults = criteria.list();

        setOfAllIds.addAll(detResults);

        // The IndividualsAssociation elements in a TaxonDescription contain DerivedUnits

        setOfAllIds.addAll(descriptionDao.getIndividualAssociationSpecimenIDs(

                associatedTaxon.getUuid(), null, null, 0, null));

        // SpecimenTypeDesignations may be associated with the TaxonName.

        setOfAllIds.addAll(taxonNameDao.getTypeSpecimenIdsForTaxonName(

                associatedTaxon.getName(), null, null, null));

        // SpecimenTypeDesignations may be associated with any HomotypicalGroup related to the specific Taxon.

        //TODO adapt to set of ids

        for(HomotypicalGroup homotypicalGroup :  associatedTaxon.getHomotypicSynonymyGroups()) {

            List<SpecimenTypeDesignation> byHomotypicalGroup = homotypicalGroupDao.getTypeDesignations(homotypicalGroup, SpecimenTypeDesignation.class, null, null, 0, null);

            for (SpecimenTypeDesignation specimenTypeDesignation : byHomotypicalGroup) {

                setOfAll.add(specimenTypeDesignation.getTypeSpecimen());

            }

        }

        if(setOfAllIds.size() == 0){