EDIT

package eu.etaxonomy.cdm.api.service;

import java.io.Serializable;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collection;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

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

import org.springframework.stereotype.Service;

import org.springframework.transaction.annotation.Transactional;

import eu.etaxonomy.cdm.api.service.config.FindOccurrencesConfigurator;

import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;

import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;

import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;

import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;

import eu.etaxonomy.cdm.filter.TaxonNodeFilter;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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

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

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

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

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

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

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

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.persistence.dao.description.IWorkingSetDao;

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

@Service

@Transactional(readOnly = false)

public class WorkingSetService extends

		AnnotatableServiceBase<WorkingSet, IWorkingSetDao> implements IWorkingSetService {

    private static Logger logger = Logger.getLogger(WorkingSetService.class);

    @Autowired

    private IOccurrenceService occurrenceService;

    @Autowired

    private ITaxonNodeService taxonNodeService;

    @Autowired

    private IProgressMonitorService progressMonitorService;

	@Override

	@Autowired

	protected void setDao(IWorkingSetDao dao) {

		this.dao = dao;

	}

	@Override

    public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(WorkingSet workingSet, Set<Feature> features, Integer pageSize,	Integer pageNumber,

			List<String> propertyPaths) {

		return dao.getDescriptionElements(workingSet, features, pageSize, pageNumber, propertyPaths);

	}

	@Override

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

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

		return dao.getTaxonFeatureDescriptionElementMap(clazz, workingSetUuid, role);

	}

	@Override

    public List<UuidAndTitleCache<WorkingSet>> getWorkingSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {

        return dao.getWorkingSetUuidAndTitleCache( limitOfInitialElements, pattern);

    }

    @Override

    @Transactional

    public UUID monitGetRowWrapper(WorkingSet workingSet) {

        RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {

            @Override

            public Serializable doRun(IRemotingProgressMonitor monitor) {

                return getRowWrapper(workingSet, monitor);

            }

        };

        UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);

        monitorThread.setPriority(3);

        monitorThread.start();

        return uuid;

    }

	@Override

	public ArrayList<RowWrapperDTO> getRowWrapper(WorkingSet workingSet, IProgressMonitor monitor) {

	    monitor.beginTask("Load row wrapper", workingSet.getDescriptions().size());

	    ArrayList<RowWrapperDTO> wrappers = new ArrayList<>();

	    Set<DescriptionBase> descriptions = workingSet.getDescriptions();

	    for (DescriptionBase description : descriptions) {

            if(monitor.isCanceled()){

                return new ArrayList<>();

            }

            wrappers.add(createRowWrapper(null, description, workingSet));

            monitor.worked(1);

        }

	    return wrappers;

	}

    @Override

    public Collection<RowWrapperDTO> loadSpecimens(WorkingSet workingSet){

        List<RowWrapperDTO> specimenCache = new ArrayList<>();

        //set filter parameters

        TaxonNodeFilter filter = TaxonNodeFilter.NewRankInstance(workingSet.getMinRank(), workingSet.getMaxRank());

        workingSet.getGeoFilter().forEach(area -> filter.orArea(area.getUuid()));

        workingSet.getTaxonSubtreeFilter().forEach(node -> filter.orSubtree(node));

        filter.setIncludeUnpublished(true);

        List<UUID> filteredNodes = taxonNodeService.uuidList(filter);

        for (UUID uuid : filteredNodes) {

            //TODO implement occurrence service for taxon nodes

            // let it return UuidAndTitleCache

            TaxonNode taxonNode = taxonNodeService.load(uuid);

            Taxon taxon = taxonNode.getTaxon();

            if(taxon!=null){

                FindOccurrencesConfigurator config = new FindOccurrencesConfigurator();

                config.setAssociatedTaxonUuid(taxon.getUuid());

                List<SpecimenOrObservationBase> specimensForTaxon = occurrenceService.findByTitle(config).getRecords();

                specimensForTaxon.forEach(specimen -> specimenCache.add(createRowWrapper(specimen, null, workingSet)));

            }

        }

        return specimenCache;

    }

	private RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptionBase description, WorkingSet workingSet){

	    if(description!=null){

	        specimen = description.getDescribedSpecimenOrObservation();

	    }

        TaxonNode taxonNode = null;

        FieldUnit fieldUnit = null;

        String identifier = null;

        NamedArea country = null;

        //supplemental information

        if(specimen!=null){

            Collection<TaxonBase<?>> associatedTaxa = occurrenceService.listAssociatedTaxa(specimen, null, null, null,

                    Arrays.asList(new String[]{

                            "taxonNodes",

                            "taxonNodes.classification",

                            }));

            if(associatedTaxa!=null){

                //FIXME: what about multiple associated taxa

                Set<TaxonNode> taxonSubtreeFilter = workingSet.getTaxonSubtreeFilter();

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

                    Taxon taxon = HibernateProxyHelper.deproxy(associatedTaxa.iterator().next(), Taxon.class);

                    taxonNode = taxon.getTaxonNode(taxonSubtreeFilter.iterator().next().getClassification());

                }

            }

            Collection<FieldUnit> fieldUnits = occurrenceService.getFieldUnits(specimen.getUuid(),

                    Arrays.asList(new String[]{

                            "gatheringEvent",

                            "gatheringEvent.country"

                            }));

            if(fieldUnits.size()!=1){

                logger.error("More than one or no field unit found for specimen"); //$NON-NLS-1$

            }

            else{

                fieldUnit = fieldUnits.iterator().next();

            }

            if(specimen instanceof DerivedUnit){

                identifier = occurrenceService.getMostSignificantIdentifier(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));

            }

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

                country = fieldUnit.getGatheringEvent().getCountry();

            }

        }

        return new RowWrapperDTO(description, specimen, taxonNode, fieldUnit, identifier, country);

	}

}