EDIT

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

import java.util.ArrayList;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.hibernate.Criteria;

import org.hibernate.Query;

import org.hibernate.Session;

import org.hibernate.criterion.Restrictions;

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

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

import org.springframework.stereotype.Repository;

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;

import eu.etaxonomy.cdm.persistence.dao.term.IDefinedTermDao;

import eu.etaxonomy.cdm.persistence.dao.term.ITermTreeDao;

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

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

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

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

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

@Repository

@Qualifier("descriptiveDataSetDaoImpl")

public class DescriptiveDataSetDao

        extends IdentifiableDaoBase<DescriptiveDataSet>

        implements IDescriptiveDataSetDao {

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

	 @Autowired

	 private ITermTreeDao termTreeDao;

	 @Autowired

     private IDefinedTermDao termDao;

	 @Autowired

     private ITaxonNodeDao nodeDao;

	public DescriptiveDataSetDao() {

		super(DescriptiveDataSet.class);

	}

	@Override

    public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,	Integer pageNumber,	List<String> propertyPaths) {

		checkNotInPriorView("DescriptiveDataSetDao.getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,Integer pageNumber, List<String> propertyPaths)");

		Query query = getSession().createQuery("SELECT description FROM DescriptiveDataSet descriptiveDataSet JOIN DescriptiveDataSet.descriptions description ORDER BY description.titleCache ASC");

		if(pageSize != null) {

			query.setMaxResults(pageSize);

	        if(pageNumber != null) {

	        	query.setFirstResult(pageNumber * pageSize);

	        } else {

	        	query.setFirstResult(0);

	        }

	    }

		@SuppressWarnings("unchecked")

        List<DescriptionBase> descriptions = query.list();

		Map<DescriptionBase, Set<DescriptionElementBase>> result = new HashMap<>();

		for(DescriptionBase description : descriptions) {

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

			criteria.add(Restrictions.eq("inDescription", description));

			if(features != null && !features.isEmpty()) {

				criteria.add(Restrictions.in("feature", features));

			}

			@SuppressWarnings("unchecked")

            List<DescriptionElementBase> r = criteria.list();

			defaultBeanInitializer.initializeAll(r, propertyPaths);

			result.put(description, new HashSet<>(r));

		}

		return result;

	}

	@Override

	public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(

	        Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {

		checkNotInPriorView("DescriptiveDataSetDao.getTaxonFeatureDescriptionElementMap(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,Integer pageNumber, List<OrderHint> orderHints,	List<String> propertyPaths)");

		Map<UuidAndTitleCache, Map<UUID, Set<T>>> result = new HashMap<>();

		try {

			//for maps see

//			http://docs.jboss.org/hibernate/core/3.3/reference/en/html/queryhql.html

//			Elements of indexed collections (arrays, lists, and maps) can be referred to by index in a where clause only:

//

//			Example: from Order order where order.items[0].id = 1234

			//feature

			String strQueryTreeId = "SELECT ws.descriptiveSystem.id FROM DescriptiveDataSet dds join dds.descriptiveSystem tree WHERE dds.uuid = :descriptiveDataSetUuid ";

			Query queryTree = getSession().createQuery(strQueryTreeId);

			queryTree.setParameter("descriptiveDataSetUuid", descriptiveDataSetUuid);

			List<?> trees = queryTree.list();

			String ftSelect = "SELECT feature.id FROM TermNode node join node.feature as feature " +

					" WHERE node.featureTree.id in (:trees) ";

			Query ftQuery = getSession().createQuery(ftSelect);

			ftQuery.setParameterList("trees", trees);

			List<?> features = ftQuery.list();

			String strClass = (clazz == null )? "DescriptionElementBase" : clazz.getSimpleName();

			String fetch = "";

			if (clazz.equals(CategoricalData.class)){

				fetch = " left join fetch el.states stateList join fetch stateList.state ";

			}else if (clazz.equals(QuantitativeData.class)){

				fetch = " left join fetch el.statisticalValues valueList join fetch valueList.type ";

			}

			String strQuery = " select taxon.uuid, taxon.id, taxon.titleCache, feature.uuid, el "

				+ " from " + strClass + " el "

				+ " join el.feature feature "

				+ " join el.inDescription d "

				+ " join d.taxon taxon "

				+ " join d.descriptiveDataSets ws "

				+ " join ws.descriptiveSystem ftree "

				+ fetch

				+ " where ws.uuid = :descriptiveDataSetUuid "

					+ " and el.class = :clazz "

					+ " and feature.id in (:features)  "

				+ " order by taxon.uuid asc, feature.uuid asc"

				;

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

			query.setParameter("descriptiveDataSetUuid", descriptiveDataSetUuid);

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

			query.setParameterList("features", features);

			//NOTE: Paging does not work with fetch

			// fill result

			@SuppressWarnings("unchecked")

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

			for (Object[] listEntry : list){

				UUID taxonUuid = (UUID)listEntry[0];

				Integer id = (Integer)listEntry[1];

				String titleCache = (String)listEntry[2];

				UuidAndTitleCache taxon = new UuidAndTitleCache(taxonUuid, id, titleCache);

				UUID featureUuid = (UUID)listEntry[3];

                T data = (T)listEntry[4];

				Map<UUID, Set<T>> taxonMap = result.get(taxon);

				if (taxonMap == null){

					taxonMap = new HashMap<>();

					result.put(taxon, taxonMap);

				}

				Set<T> featureSet = taxonMap.get(featureUuid);

				if (featureSet == null){

					featureSet = new HashSet<>();

					taxonMap.put(featureUuid, featureSet);

				}else{

					if (logger.isDebugEnabled()){logger.debug("feature set already exists");}

				}

				featureSet.add(data);

			}

//			defaultBeanInitializer.initialize(

			return result;

		} catch (Exception e) {

			e.printStackTrace();

			throw new RuntimeException(e);

		}

	}

    /**

     * {@inheritDoc}

     */

    @Override

    public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements,

            String pattern) {

        Session session = getSession();

        String queryString = "SELECT uuid, id, label FROM DescriptiveDataSet ";

        if ( pattern != null){

            queryString += " WHERE ";

            queryString += " label LIKE :pattern";

        }

        Query query;

        query = session.createQuery(queryString);

        if (limitOfInitialElements != null){

            query.setMaxResults(limitOfInitialElements);

        }

        if (pattern != null){

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

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

              pattern = pattern + "%";

              query.setParameter("pattern", pattern);

        }

        @SuppressWarnings("unchecked")

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

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

        for(Object[] object : result){

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

        }

        return list;

    }

    private List<UUID> getNodeUuidsForDescriptiveDataSet(UUID uuid) {

        Session session = getSession();

        String queryString = "SELECT t.uuid  FROM DescriptiveDataSet a JOIN a.taxonSubtreeFilter as t WHERE a.uuid = :uuid";

        Query query;

        query = session.createQuery(queryString);

        query.setParameter("uuid", uuid);

        @SuppressWarnings("unchecked")

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

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

        for(UUID object : result){

            list.add(object);

        }

        return list;

    }

    @Override

    public DescriptiveDataSetBaseDto getDescriptiveDataSetDtoByUuid(UUID uuid) {

        String queryString = DescriptiveDataSetBaseDto.getDescriptiveDataSetDtoSelect()

                + " WHERE a.uuid = :uuid"

                + " ORDER BY a.titleCache";

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

        query.setParameter("uuid", uuid);

        @SuppressWarnings("unchecked")

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

        List<DescriptiveDataSetBaseDto> list = DescriptiveDataSetBaseDto.descriptiveDataSetBaseDtoListFrom(result);

        UUID descriptiveSystemUuid = null;

        UUID minRankUuid = null;

        UUID maxRankUuid = null;

        if (result != null && !result.isEmpty()){

            Object[] descriptiveDataSetResult = result.get(0);

            descriptiveSystemUuid = (UUID)descriptiveDataSetResult[4];

            minRankUuid = (UUID)descriptiveDataSetResult[5];

            maxRankUuid = (UUID)descriptiveDataSetResult[6];

        }else{

            return null;

        }

        //get descriptiveSystem

        DescriptiveDataSetBaseDto dto = list.get(0);

        if (descriptiveSystemUuid != null){

            TermTreeDto treeDto = termTreeDao.getTermTreeDtosByUuid(descriptiveSystemUuid);

            dto.setDescriptiveSystem(treeDto);

        }

        //get taxon nodes

        List<UUID> nodeUuids = getNodeUuidsForDescriptiveDataSet(uuid);

        List<TaxonNodeDto> nodeDtos = nodeDao.getTaxonNodeDtos(nodeUuids);

        Set<TaxonNodeDto> nodeSet = new HashSet<>(nodeDtos);

        dto.setSubTreeFilter(nodeSet);

        TermDto minRank = termDao.getTermDto(minRankUuid);

        TermDto maxRank = termDao.getTermDto(maxRankUuid);

        dto.setMaxRank(maxRank);

        dto.setMinRank(minRank);

        return dto;

    }

}