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.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.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.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.UuidAndTitleCache;

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

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

/**

 * @author a.babadshanjan

 * @created 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 int 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()).intValue();

    }

    @Override

    public int countDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase) {

        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));

            }

            criteria.setProjection(Projections.rowCount());

            return ((Number)criteria.uniqueResult()).intValue();

        } 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()));

            }

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

            return ((Long)query.getSingleResult()).intValue();

        }

    }

    @Override

    public int 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()).intValue();

    }

    @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);

        if(pageSize != null) {

            query.setMaxResults(pageSize);

            if(pageNumber != null) {

                query.setFirstResult(pageNumber * pageSize);

            } else {

                query.setFirstResult(0);

            }

        }

        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));

            }

            if(pageSize != null) {

                criteria.setMaxResults(pageSize);

                if(pageNumber != null) {

                    criteria.setFirstResult(pageNumber * pageSize);

                } else {

                    criteria.setFirstResult(0);

                }

            }

            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()));

            }

            if(pageSize != null) {

                query.setMaxResults(pageSize);

                if(pageNumber != null) {

                    query.setFirstResult(pageNumber * pageSize);

                } else {

                    query.setFirstResult(0);

                }

            }

            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);

        if(pageSize != null) {

            query.setMaxResults(pageSize);

            if(pageNumber != null) {

                query.setFirstResult(pageNumber * pageSize);

            } else {

                query.setFirstResult(0);

            }

        }

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

        Criteria criteria = null;

        if(clazz == null) {

            criteria = getSession().createCriteria(type);

        } else {

            criteria = getSession().createCriteria(clazz);

        }

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

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

        return ((Number)criteria.uniqueResult()).intValue();

    }

    @Override

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

        }

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

        if(limit != null) {

            if(start != null) {

                criteria.setFirstResult(start);

            } else {

                criteria.setFirstResult(0);

            }

            criteria.setMaxResults(limit);

        }

        addOrder(criteria,orderHints);

        @SuppressWarnings("unchecked")

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

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

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

        Criteria criteria = null;

        if(clazz == null) {

            criteria = getSession().createCriteria(type);

        } else {

            criteria = getSession().createCriteria(clazz);

        }

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

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

        return ((Number)criteria.uniqueResult()).intValue();

    }

    @Override

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

        }

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

        if(limit != null) {

            if(start != null) {

                criteria.setFirstResult(start);

            } else {

                criteria.setFirstResult(0);

            }

            criteria.setMaxResults(limit);

        }

        addOrder(criteria,orderHints);

        @SuppressWarnings("unchecked")

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

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @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){

            if(limit != null) {

                if(start != null) {

                    criteria.setFirstResult(start);

                } else {

                    criteria.setFirstResult(0);

                }

                criteria.setMaxResults(limit);

            }

            if(orderHints!=null){

                addOrder(criteria,orderHints);

            }

            @SuppressWarnings("unchecked")

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

            defaultBeanInitializer.initializeAll(results, propertyPaths);

            return results;

        }

        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<? extends SpecimenOrObservationBase> associatedTaxaList = listByAssociatedTaxon(clazz, associatedTaxon, limit, start, orderHints, propertyPaths);

            if(associatedTaxaList!=null){

                for (SpecimenOrObservationBase specimenOrObservationBase : associatedTaxaList) {

                    associationUuids.add(specimenOrObservationBase.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;

            }

        }

        return criteria;

    }

    @Override

    public <T extends SpecimenOrObservationBase> int 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 ((Number)criteria.uniqueResult()).intValue();

        }

        return 0;

    }

    @Override

    public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {

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

        Session session = getSession();

        Query query = session.createQuery("select uuid, id, titleCache from " + type.getSimpleName() + " where NOT dtype = " + FieldUnit.class.getSimpleName());

        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<UuidAndTitleCache<FieldUnit>>();

        Session session = getSession();

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

        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) {

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

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

        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";

        }

        if(orderHints != null && orderHints.size() > 0){

            queryString += " order by ";

            String orderStr = "";

            for(OrderHint orderHint : orderHints){

                if(orderStr.length() > 0){

                    orderStr += ", ";

                }

                queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();

            }

            queryString += orderStr;

        }

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

        query.setParameterList("setOfAll", setOfAll);

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

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

        }

        if(limit != null) {

            if(start != null) {

                query.setFirstResult(start);

            } else {

                query.setFirstResult(0);

            }

            query.setMaxResults(limit);

        }

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

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

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

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

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

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

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

        setOfAll.addAll(byDetermination);

        //check also for synonyms

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

            setOfAll.addAll(list(type, synonym, null, 0, null, null));

        }

        //check also for name determinations

        setOfAll.addAll(list(type, associatedTaxon.getName(), null, 0, null, null));

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

            setOfAll.addAll(list(type, synonymName, null, 0, null, null));

        }

        // The IndividualsAssociation elements in a TaxonDescription contain DerivedUnits

        List<IndividualsAssociation> byIndividualsAssociation = descriptionDao.getDescriptionElementForTaxon(

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

        for(IndividualsAssociation individualsAssociation : byIndividualsAssociation){

            setOfAll.add(individualsAssociation.getAssociatedSpecimenOrObservation());

        }

        // SpecimenTypeDesignations may be associated with the TaxonName.

        List<SpecimenTypeDesignation> bySpecimenTypeDesignation = taxonNameDao.getTypeDesignations(associatedTaxon.getName(),

                SpecimenTypeDesignation.class, null, null, 0, null);

        for (SpecimenTypeDesignation specimenTypeDesignation : bySpecimenTypeDesignation) {

            setOfAll.add(specimenTypeDesignation.getTypeSpecimen());

        }

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

        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(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";

        }

        if(orderHints != null && orderHints.size() > 0){

            queryString += " order by ";

            String orderStr = "";

            for(OrderHint orderHint : orderHints){

                if(orderStr.length() > 0){

                    orderStr += ", ";

                }

                queryString += "sob." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();

            }

            queryString += orderStr;

        }

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

        query.setParameterList("setOfAll", setOfAll);

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

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

        }

        if(limit != null) {

            if(start != null) {

                query.setFirstResult(start);

            } else {

                query.setFirstResult(0);

            }

            query.setMaxResults(limit);

        }

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

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public Collection<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        String queryString = "FROM SpecimenOrObservationBase specimens WHERE specimens.recordBasis = :type";

        if(orderHints != null && orderHints.size() > 0){

            queryString += " order by ";

            String orderStr = "";

            for(OrderHint orderHint : orderHints){

                if(orderStr.length() > 0){

                    orderStr += ", ";

                }

                queryString += "specimens." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();

            }

            queryString += orderStr;

        }

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

        query.setParameter("type", type);

        if(limit != null) {

            if(start != null) {

                query.setFirstResult(start);

            } else {

                query.setFirstResult(0);

            }

            query.setMaxResults(limit);

        }

        List results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        String queryString = "FROM DeterminationEvent determination WHERE determination.identifiedUnit = :specimen";

        if(orderHints != null && orderHints.size() > 0){

            queryString += " order by ";

            String orderStr = "";

            for(OrderHint orderHint : orderHints){

                if(orderStr.length() > 0){

                    orderStr += ", ";

                }

                queryString += "determination." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();

            }

            queryString += orderStr;

        }

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

        query.setParameter("specimen", specimen);

        if(limit != null) {

            if(start != null) {

                query.setFirstResult(start);

            } else {

                query.setFirstResult(0);

            }

            query.setMaxResults(limit);

        }

        List results = query.list();

        defaultBeanInitializer.initializeAll(results, propertyPaths);

        return results;

    }

    @Override

    public Collection<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> specimen, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths) {

        String queryString = "FROM SpecimenTypeDesignation designations WHERE designations.typeSpecimen = :specimen";

        if(orderHints != null && orderHints.size() > 0){

            queryString += " order by ";

            String orderStr = "";

            for(OrderHint orderHint : orderHints){

                if(orderStr.length() > 0){

                    orderStr += ", ";

                }

                queryString += "designations." + orderHint.getPropertyName() + " " + orderHint.getSortOrder().toHql();

            }

            queryString += orderStr;

        }

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

        query.setParameter("specimen", specimen);

        if(limit != null) {

            if(start != null) {