EDIT

package eu.etaxonomy.cdm.api.service;

import java.math.BigDecimal;

import java.util.ArrayList;

import java.util.Arrays;

import java.util.Collection;

import java.util.Collections;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Optional;

import java.util.Set;

import java.util.UUID;

import java.util.stream.Collectors;

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.UpdateResult.Status;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.filter.TaxonNodeFilter;

import eu.etaxonomy.cdm.format.description.DefaultCategoricalDescriptionBuilder;

import eu.etaxonomy.cdm.format.description.DefaultQuantitativeDescriptionBuilder;

import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;

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

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

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.DescriptionType;

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.IndividualsAssociation;

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

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

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

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

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

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

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.reference.CdmLinkSource;

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

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.IDescriptiveDataSetDao;

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;

import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGenerator;

import eu.etaxonomy.cdm.strategy.generate.PolytomousKeyGeneratorConfigurator;

@Service

@Transactional(readOnly=true)

public class DescriptiveDataSetService

        extends IdentifiableServiceBase<DescriptiveDataSet, IDescriptiveDataSetDao>

        implements IDescriptiveDataSetService {

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

    @Autowired

    private IOccurrenceService occurrenceService;

    @Autowired

    private ITaxonService taxonService;

    @Autowired

    private IPolytomousKeyService polytomousKeyService;

    @Autowired

    private IDefinedTermDao termDao;

    @Autowired

    private IDescriptionService descriptionService;

    @Autowired

    private ITaxonNodeService taxonNodeService;

	@Override

	@Autowired

	protected void setDao(IDescriptiveDataSetDao dao) {

		this.dao = dao;

	}

	@Override

    public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,	Integer pageNumber,

			List<String> propertyPaths) {

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

	}

	@Override

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

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

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

	}

	@Override

    public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {

        return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern);

    }

	@Override

	public ArrayList<RowWrapperDTO> getRowWrapper(UUID descriptiveDataSetUuid, IProgressMonitor monitor) {

	    DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid);

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

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

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

	    for (DescriptionBase description : descriptions) {

            if(monitor.isCanceled()){

                return new ArrayList<>();

            }

            RowWrapperDTO rowWrapper = null;

            // only viable descriptions are aggregated, literature or default descriptions

            if(HibernateProxyHelper.isInstanceOf(description, TaxonDescription.class) &&

                    (description.isAggregatedStructuredDescription()

                            || description.getTypes().contains(DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION)

                            || description.getTypes().contains(DescriptionType.SECONDARY_DATA)

                            )){

                rowWrapper = createTaxonRowWrapper(description.getUuid(), descriptiveDataSet.getUuid());

            }

            else if (HibernateProxyHelper.isInstanceOf(description, SpecimenDescription.class)&&

                    !description.getTypes().contains(DescriptionType.CLONE_FOR_SOURCE)){

                rowWrapper = createSpecimenRowWrapper(HibernateProxyHelper.deproxy(description, SpecimenDescription.class), descriptiveDataSetUuid);

            }

            if(rowWrapper!=null){

                wrappers.add(rowWrapper);

            }

            monitor.worked(1);

        }

	    return wrappers;

	}

    @Override

    public Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet){

        List<UUID> filteredNodes = findFilteredTaxonNodes(descriptiveDataSet);

        if(filteredNodes.isEmpty()){

            return Collections.EMPTY_SET;

        }

        Collection<SpecimenNodeWrapper> result = occurrenceService.listUuidAndTitleCacheByAssociatedTaxon(filteredNodes, null, null);

        return result;

    }

    @Override

    public Collection<SpecimenNodeWrapper> loadSpecimens(UUID descriptiveDataSetUuid){

        DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);

        return loadSpecimens(dataSet);

    }

    @Override

    public List<UUID> findFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet){

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

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

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

        filter.setIncludeUnpublished(true);

        return taxonNodeService.uuidList(filter);

    }

    @Override

    public List<TaxonNode> loadFilteredTaxonNodes(DescriptiveDataSet descriptiveDataSet, List<String> propertyPaths){

        return taxonNodeService.load(findFilteredTaxonNodes(descriptiveDataSet), propertyPaths);

    }

    @Override

    public TaxonDescription findDefaultDescription(UUID specimenDescriptionUuid, UUID dataSetUuid){

        SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescriptionUuid);

        DescriptiveDataSet dataSet = load(dataSetUuid);

        TaxonNode node = findTaxonNodeForDescription(specimenDescription, dataSet);

        return recurseDefaultDescription(node, dataSet);

    }

    private TaxonDescription recurseDefaultDescription(TaxonNode node, DescriptiveDataSet dataSet){

        TaxonDescription defaultDescription = null;

        if(node!=null && node.getTaxon()!=null){

            defaultDescription = findTaxonDescriptionByDescriptionType(dataSet, node.getTaxon(), DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION);

            if(defaultDescription==null && node.getParent()!=null){

                defaultDescription = recurseDefaultDescription(node.getParent(), dataSet);

            }

        }

        return defaultDescription;

    }

    private TaxonNode findTaxonNodeForDescription(SpecimenDescription description, DescriptiveDataSet descriptiveDataSet){

        SpecimenOrObservationBase specimen = description.getDescribedSpecimenOrObservation();

        //get taxon node

        Set<IndividualsAssociation> associations = (Set<IndividualsAssociation>)descriptiveDataSet.getDescriptions()

                .stream()

                .flatMap(desc->desc.getElements().stream())// put all description element in one stream

                .filter(element->element instanceof IndividualsAssociation)

                .map(ia->(IndividualsAssociation)ia)

                .collect(Collectors.toSet());

        Classification classification = descriptiveDataSet.getTaxonSubtreeFilter().iterator().next().getClassification();

        for (IndividualsAssociation individualsAssociation : associations) {

            if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(specimen)){

                return ((TaxonDescription) individualsAssociation.getInDescription()).getTaxon().getTaxonNode(classification);

            }

        }

        return null;

    }

    @Override

    public TaxonRowWrapperDTO createTaxonRowWrapper(UUID taxonDescriptionUuid, UUID descriptiveDataSetUuid) {

        TaxonNode taxonNode = null;

        Classification classification = null;

        TaxonDescription description = (TaxonDescription) descriptionService.load(taxonDescriptionUuid,

                Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature"));

        DescriptiveDataSet descriptiveDataSet = dao.load(descriptiveDataSetUuid, null);

        Optional<TaxonNode> first = descriptiveDataSet.getTaxonSubtreeFilter().stream()

                .filter(node->node.getClassification()!=null).findFirst();

        Optional<Classification> classificationOptional = first.map(node->node.getClassification());

        Set<DescriptionBaseDto> descriptions = new HashSet<>();

        if(classificationOptional.isPresent()){

            classification = classificationOptional.get();

            Taxon taxon = (Taxon) taxonService.load(description.getTaxon().getId(), Arrays.asList("taxonNodes", "taxonNodes.classification"));

            taxonNode = taxon.getTaxonNode(classification);

            for (DescriptionBase desc: taxon.getDescriptions()){

                descriptions.add(new DescriptionBaseDto(desc));

            }

        }

        return new TaxonRowWrapperDTO(new DescriptionBaseDto(description), new TaxonNodeDto(taxonNode), descriptions);

    }

    @Override

    @Transactional(readOnly=false)

    public UpdateResult addRowWrapperToDataset(Collection<SpecimenRowWrapperDTO> wrappers, UUID datasetUuid){

        UpdateResult result = new UpdateResult();

        DescriptiveDataSet dataSet = load(datasetUuid);

        result.setCdmEntity(dataSet);

        List<UUID> taxonUuids = wrappers.stream().map(wrapper->wrapper.getTaxonNode().getTaxonUuid()).collect(Collectors.toList());

        List<TaxonBase> taxa = taxonService.load(taxonUuids, Arrays.asList(new String[]{"descriptions"}));

        for (SpecimenRowWrapperDTO wrapper : wrappers) {

            Optional<TaxonBase> findAny = taxa.stream().filter(taxon->taxon.getUuid().equals(wrapper.getTaxonNode().getTaxonUuid())).findAny();

            if(!findAny.isPresent()){

                result.addException(new IllegalArgumentException("Could not create wrapper for "+ wrapper.getSpecimen().getLabel()));

                continue;

            }

            Taxon taxon = (Taxon) findAny.get();

//            UUID taxonDescriptionUuid = wrapper..getTaxonDescriptionUuid();

            TaxonDescription taxonDescription = null;

//            if(taxonDescriptionUuid!=null){

//                taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);

//            }

            SpecimenOrObservationBase specimen = occurrenceService.load(wrapper.getSpecimen().getUuid());

            if(taxonDescription==null){

                Optional<TaxonDescription> associationDescriptionOptional = taxon.getDescriptions().stream()

                        .filter(desc->desc.getTypes().contains(DescriptionType.INDIVIDUALS_ASSOCIATION))

                        .findFirst();

                if(!associationDescriptionOptional.isPresent()){

                    taxonDescription = TaxonDescription.NewInstance(taxon);

                }

                else{

                    taxonDescription = associationDescriptionOptional.get();

                }

                IndividualsAssociation association = IndividualsAssociation.NewInstance(specimen);

                taxonDescription.addElement(association);

                taxonService.saveOrUpdate(taxon);

                result.addUpdatedObject(taxon);

            }

            DescriptionBase specimenDescription = wrapper.getDescription().getDescription();

            if (specimenDescription.isPersited()){

                specimenDescription = descriptionService.load(specimenDescription.getUuid());

            }else {

                specimen.addDescription(specimenDescription);

            }

//            SpecimenRowWrapperDTO rowWrapper = createSpecimenRowWrapper(specimenDescription, wrapper.getTaxonNode().getUuid(), datasetUuid);

            if(wrapper==null){

                result.addException(new IllegalArgumentException("Could not create wrapper for "+wrapper.getDescription().getDescription()));

                continue;

            }

            //add specimen description to data set

//            specimenDescription = (SpecimenDescription) descriptionService.load(rowWrapper.getDescription().getDescription().getUuid());

            specimenDescription.addDescriptiveDataSet(dataSet);

            //add taxon description with IndividualsAssociation to the specimen to data set

            taxonDescription.addDescriptiveDataSet(dataSet);

            result.addUpdatedObject(specimen);

            result.addUpdatedObject(specimenDescription);

            result.addUpdatedObject(taxonDescription);

        }

        saveOrUpdate(dataSet);

        return result;

    }

    private SpecimenRowWrapperDTO createSpecimenRowWrapper(SpecimenDescription description, UUID taxonNodeUuid,

            UUID datasetUuid) {

        TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);

        DescriptiveDataSet descriptiveDataSet = load(datasetUuid);

        SpecimenOrObservationBase specimen = HibernateProxyHelper.deproxy(description.getDescribedSpecimenOrObservation(), SpecimenOrObservationBase.class);

        //supplemental information

        if(taxonNode==null){

            taxonNode = findTaxonNodeForDescription(description, descriptiveDataSet);

        }

        FieldUnit fieldUnit = null;

        String identifier = null;

        NamedArea country = null;

        if(taxonNode==null){

            return null;

        }

        //taxon node was found

        //get field unit

        Collection<FieldUnit> fieldUnits = occurrenceService.findFieldUnits(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"); //$NON-NLS-1$

            return null;

        }

        else{

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

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

            }

        }

        //get identifier

        if(HibernateProxyHelper.isInstanceOf(specimen, DerivedUnit.class)){

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

        }

        //get country

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

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

        }

        //get default taxon description

//        TaxonDescription defaultTaxonDescription = findDefaultDescription(description.getUuid(), descriptiveDataSet.getUuid());

        TaxonDescription defaultTaxonDescription = recurseDefaultDescription(taxonNode, descriptiveDataSet);

        TaxonRowWrapperDTO taxonRowWrapper = defaultTaxonDescription != null

                ? createTaxonRowWrapper(defaultTaxonDescription.getUuid(), descriptiveDataSet.getUuid()) : null;

//                use description not specimen for specimenRow

        SpecimenRowWrapperDTO specimenRowWrapperDTO = new SpecimenRowWrapperDTO(new DescriptionBaseDto(description), specimen.getRecordBasis(), new TaxonNodeDto(taxonNode), fieldUnit, identifier, country);

        specimenRowWrapperDTO.setDefaultDescription(taxonRowWrapper);

        return specimenRowWrapperDTO;

    }

    @Override

    public SpecimenRowWrapperDTO createSpecimenRowWrapper(SpecimenDescription description, UUID descriptiveDataSetUuid){

        return createSpecimenRowWrapper(description, null, descriptiveDataSetUuid);

	}

    @Override

    public SpecimenRowWrapperDTO createSpecimenRowWrapper(UUID specimenUuid, UUID taxonNodeUuid, UUID descriptiveDataSetUuid){

        SpecimenOrObservationBase<?> specimen = occurrenceService.load(specimenUuid);

        SpecimenDescription specimenDescription = findSpecimenDescription(descriptiveDataSetUuid, specimen, true);

        return createSpecimenRowWrapper(specimenDescription, taxonNodeUuid, descriptiveDataSetUuid);

    }

    @Override

    @Transactional(readOnly = false)

    public UpdateResult updateCaches(Class<? extends DescriptiveDataSet> clazz, Integer stepSize,

            IIdentifiableEntityCacheStrategy<DescriptiveDataSet> cacheStrategy, IProgressMonitor monitor) {

        if (clazz == null) {

            clazz = DescriptiveDataSet.class;

        }

        return super.updateCachesImpl(clazz, stepSize, cacheStrategy, monitor);

    }

    private TaxonDescription findTaxonDescriptionByDescriptionType(DescriptiveDataSet dataSet, Taxon taxon, DescriptionType descriptionType){

        Optional<TaxonDescription> first = taxon.getDescriptions().stream()

                .filter(desc -> desc.getTypes().stream().anyMatch(type -> type.equals(descriptionType)))

                .filter(desc -> dataSet.getDescriptions().contains(desc))

                .findFirst();

        if(first.isPresent()){

            return HibernateProxyHelper.deproxy(descriptionService.load(first.get().getUuid(),

                  Arrays.asList("taxon", "descriptionElements", "descriptionElements.feature")), TaxonDescription.class);

        }

        return null;

    }

    @Override

    public TaxonDescription findTaxonDescriptionByDescriptionType(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){

        DescriptiveDataSet dataSet = load(dataSetUuid);

        TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid);

        return findTaxonDescriptionByDescriptionType(dataSet, taxonNode.getTaxon(), descriptionType);

    }

    @Override

    @Transactional(readOnly=false)

    public UpdateResult generatePolytomousKey(UUID descriptiveDataSetUuid, UUID taxonUuid) {

        UpdateResult result = new UpdateResult();

        PolytomousKeyGeneratorConfigurator keyConfig = new PolytomousKeyGeneratorConfigurator();

        DescriptiveDataSet descriptiveDataSet = load(descriptiveDataSetUuid);

        keyConfig.setDataSet(descriptiveDataSet);

        PolytomousKey key = new PolytomousKeyGenerator().invoke(keyConfig);

        IdentifiableServiceConfiguratorImpl<PolytomousKey> serviceConfig= new IdentifiableServiceConfiguratorImpl<>();

        serviceConfig.setTitleSearchString(descriptiveDataSet.getTitleCache());

        List<PolytomousKey> list = polytomousKeyService.findByTitle(serviceConfig).getRecords();

        if(list!=null){

            list.forEach(polytomousKey->polytomousKeyService.delete(polytomousKey));

        }

        key.setTitleCache(descriptiveDataSet.getTitleCache(), true);

        Taxon taxon = (Taxon) taxonService.load(taxonUuid);

        key.addTaxonomicScope(taxon);

        polytomousKeyService.saveOrUpdate(key);

        result.setCdmEntity(key);

        result.addUpdatedObject(taxon);

        return result;

    }

    @Override

    @Transactional(readOnly=false)

    public DeleteResult removeDescription(UUID descriptionUuid, UUID descriptiveDataSetUuid, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {

        DeleteResult result = new DeleteResult();

        DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);

        DescriptionBase descriptionBase = descriptionService.load(descriptionUuid);

        if(dataSet==null || descriptionBase==null){

            result.setError();

        }

        else{

            removeDescriptionFromDataSet(result, dataSet, descriptionBase, config);

        }

        return result;

    }

    @Override

    @Transactional(readOnly=false)

    public DeleteResult removeDescriptions(List<UUID> descriptionUuids, UUID descriptiveDataSetUuid, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {

        DeleteResult result = new DeleteResult();

        DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);

        List<DescriptionBase> descriptions = descriptionService.load(descriptionUuids, null);

        if(dataSet==null || descriptions==null){

            result.setError();

        }

        else{

            for (DescriptionBase description: descriptions){

                removeDescriptionFromDataSet(result, dataSet, description, config);

            }

        }

        return result;

    }

    /**

     * @param result

     * @param dataSet

     * @param description

     */

    private void removeDescriptionFromDataSet(DeleteResult result, DescriptiveDataSet dataSet,

            DescriptionBase description, RemoveDescriptionsFromDescriptiveDataSetConfigurator config) {

        if (description == null){

            return;

        }

        boolean success = dataSet.removeDescription(description);

        result.addDeletedObject(description);// remove taxon description with IndividualsAssociation from data set

        if(description instanceof SpecimenDescription){

            @SuppressWarnings("cast")

            Set<IndividualsAssociation> associations = (Set<IndividualsAssociation>)dataSet.getDescriptions()

                    .stream()

                    .flatMap(desc->desc.getElements().stream())// put all description element in one stream

                    .filter(element->element instanceof IndividualsAssociation)

                    .map(ia->(IndividualsAssociation)ia)

                    .collect(Collectors.toSet());

            Classification classification = dataSet.getTaxonSubtreeFilter().iterator().next().getClassification();

            for (IndividualsAssociation individualsAssociation : associations) {

                if(individualsAssociation.getAssociatedSpecimenOrObservation().equals(description.getDescribedSpecimenOrObservation())){

                    dataSet.removeDescription(individualsAssociation.getInDescription());

                    result.addUpdatedObject(individualsAssociation.getInDescription());

                }

            }

        }

        if (description instanceof TaxonDescription){

            UUID taxonUuid = ((TaxonDescription)description).getTaxon().getUuid();

            DeleteResult isDeletable = descriptionService.isDeletable(description.getUuid());

            for (CdmBase relatedCdmBase: isDeletable.getRelatedObjects()){

                if (relatedCdmBase instanceof CdmLinkSource){

                    CdmLinkSource linkSource = (CdmLinkSource)relatedCdmBase;

                    if (linkSource.getTarget().equals(this)){

                    }

                }

            }

        }

        if (!config.isOnlyRemoveDescriptionsFromDataSet()){

            DeleteResult deleteResult = descriptionService.deleteDescription(description);

            result.includeResult(deleteResult);

            result.addUpdatedObject(dataSet);

        }else{

            MergeResult<DescriptiveDataSet> mergeResult = dao.merge(dataSet, true);

            result.addUpdatedObject(mergeResult.getMergedEntity());

        }

        result.setStatus(success?Status.OK:Status.ERROR);

    }

    @Override

    @Transactional(readOnly = false)

    public DeleteResult delete(UUID datasetUuid, DeleteDescriptiveDataSetConfigurator config,  IProgressMonitor monitor){

        DescriptiveDataSet dataSet = dao.load(datasetUuid);

        monitor.beginTask("Delete Descriptive Dataset", dataSet.getDescriptions().size() +1);

        DeleteResult result = new DeleteResult();

        DeleteResult descriptionResult = new DeleteResult();

        if (!dataSet.getDescriptions().isEmpty()){

            Set<DescriptionBase> descriptions = new HashSet();;

            for (DescriptionBase desc: dataSet.getDescriptions()){

                descriptions.add(desc);

            }

            monitor.subTask("Delete descriptions");

            for (DescriptionBase desc: descriptions){

                dataSet.removeDescription(desc);

                if (desc instanceof SpecimenDescription && config.isDeleteAllSpecimenDescriptions()){

                    descriptionResult.includeResult(descriptionService.deleteDescription(desc));

                }else if (desc instanceof TaxonDescription){

                    if( desc.getTypes().contains(DescriptionType.DEFAULT_VALUES_FOR_AGGREGATION) && config.isDeleteAllDefaultDescriptions()){

                        descriptionResult.includeResult(descriptionService.deleteDescription(desc));

                    }else if (desc.getTypes().contains(DescriptionType.SECONDARY_DATA) && config.isDeleteAllLiteratureDescriptions()){

                        descriptionResult.includeResult(descriptionService.deleteDescription(desc));

                    }else if (desc.getTypes().contains(DescriptionType.AGGREGATED_STRUC_DESC) && config.isDeleteAllAggregatedDescriptions()){

                        descriptionResult.includeResult(descriptionService.deleteDescription(desc));

                    }

                }

            }

        }

        UUID uuid = dao.delete(dataSet);

        monitor.worked(1);

        monitor.done();

        result.includeResult(descriptionResult);

        result.setStatus(Status.OK);

        result.addDeletedObject(dataSet);

        return result;

    }

    @Override

    @Transactional(readOnly=false)

    public TaxonRowWrapperDTO createTaxonDescription(UUID dataSetUuid, UUID taxonNodeUuid, DescriptionType descriptionType){

        DescriptiveDataSet dataSet = load(dataSetUuid);

        TaxonNode taxonNode = taxonNodeService.load(taxonNodeUuid, Arrays.asList("taxon"));

        TaxonDescription newTaxonDescription = TaxonDescription.NewInstance(taxonNode.getTaxon());

        newTaxonDescription.setTitleCache(dataSet.getLabel()+": "+newTaxonDescription.generateTitle(), true); //$NON-NLS-2$

        newTaxonDescription.getTypes().add(descriptionType);

        dataSet.getDescriptiveSystem().getDistinctTerms().forEach(wsFeature->{

            if(wsFeature.isSupportsCategoricalData()){

                newTaxonDescription.addElement(CategoricalData.NewInstance(wsFeature));

            }

            else if(wsFeature.isSupportsQuantitativeData()){

                newTaxonDescription.addElement(QuantitativeData.NewInstance(wsFeature));

            }

        });

        dataSet.addDescription(newTaxonDescription);

        saveOrUpdate(dataSet);

        return createTaxonRowWrapper(newTaxonDescription.getUuid(), dataSet.getUuid());

    }

    @Override

    public List<TermDto> getSupportedStatesForFeature(UUID featureUuid){

        return termDao.getSupportedStatesForFeature(featureUuid);

    }

    @Override

    @Transactional(readOnly=false)

    public SpecimenDescription findSpecimenDescription(UUID descriptiveDataSetUuid, SpecimenOrObservationBase specimen, boolean addDatasetSource){

        DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);

//        SpecimenOrObservationBase specimen = occurrenceService.load(specimenUuid);

        Set<? extends Feature> datasetFeatures = dataSet.getDescriptiveSystem().getDistinctTerms();

        List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();

        for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {

            specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescription.getUuid());

            //check if description is already added to data set

            if(dataSet.getDescriptions().contains(specimenDescription) ){

                return specimenDescription;

            }

            //gather specimen description features and check for match with dataset features

            Set<Feature> specimenDescriptionFeatures = new HashSet<>();

            for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {

                Feature feature = specimenDescriptionElement.getFeature();

                specimenDescriptionFeatures.add(feature);

                if(datasetFeatures.contains(feature) && RowWrapperDTO.hasData(specimenDescriptionElement)){

                    matchingDescriptionElements.add(specimenDescriptionElement);

                }

            }

        }

        //Create new specimen description if description has not already been added to the dataset

        SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);

        newDesription.setTitleCache("Dataset "+dataSet.getLabel()+": "+newDesription.generateTitle(), true); //$NON-NLS-2$

        //check for equals description element (same feature and same values)

        Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();

        for(DescriptionElementBase element:matchingDescriptionElements){

            List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());

            if(list==null){

                list = new ArrayList<>();

            }

            list.add(element);

            featureToElementMap.put(element.getFeature(), list);

        }

        Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();

        for(Feature feature:featureToElementMap.keySet()){

            List<DescriptionElementBase> elements = featureToElementMap.get(feature);

            //no duplicate description elements found for this feature

            if(elements.size()==1){

                descriptionElementsToClone.add(elements.get(0));

            }

            //duplicates found -> check if all are equal

            else{

                DescriptionElementBase match = null;

                for (DescriptionElementBase descriptionElementBase : elements) {

                    if(match==null){

                        match = descriptionElementBase;

                    }

                    else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){

                        match = null;

                        //TODO: propagate message

//                        MessagingUtils.informationDialog(Messages.CharacterMatrix_MULTIPLE_DATA,

//                                String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));

                        break;

                    }

                }

                if(match!=null){

                    descriptionElementsToClone.add(match);

                }

            }

        }

        //clone matching descriptionElements

        for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {

            DescriptionElementBase clone;

            try {

                clone = descriptionElementBase.clone(newDesription);

                clone.getSources().forEach(source -> {

                    if(descriptionElementBase instanceof CategoricalData){

                        TextData label = new DefaultCategoricalDescriptionBuilder().build((CategoricalData) descriptionElementBase, Arrays.asList(new Language[]{Language.DEFAULT()}));

                        source.setOriginalNameString(label.getText(Language.DEFAULT()));

                    }

                    else if(descriptionElementBase instanceof QuantitativeData){

                        TextData label = new DefaultQuantitativeDescriptionBuilder().build((QuantitativeData) descriptionElementBase, Arrays.asList(new Language[]{Language.DEFAULT()}));

                        source.setOriginalNameString(label.getText(Language.DEFAULT()));

                    }

                });

            } catch (CloneNotSupportedException e) {

                //nothing

            }

        }

        //add sources of data set

        if(addDatasetSource){

            dataSet.getSources().forEach(source->{

                try {

                    newDesription.addSource(source.clone());

                } catch (CloneNotSupportedException e) {

                    //nothing

                }

            });

        }

        return newDesription;

    }

    //TODO: this should either be solved in the model class itself

    //OR this should cover all possibilities including modifiers for example

    private class DescriptionElementCompareWrapper {

        private DescriptionElementBase element;

        private Set<UUID> stateUuids = new HashSet<>();

        private Set<BigDecimal> avgs = new HashSet<>();

        private Set<BigDecimal> exacts = new HashSet<>();

        private Set<BigDecimal> maxs = new HashSet<>();

        private Set<BigDecimal> mins = new HashSet<>();

        private Set<BigDecimal> sampleSizes = new HashSet<>();

        private Set<BigDecimal> standardDevs = new HashSet<>();

        private Set<BigDecimal> lowerBounds = new HashSet<>();

        private Set<BigDecimal> upperBounds = new HashSet<>();

        private Set<BigDecimal> variances = new HashSet<>();

        public DescriptionElementCompareWrapper(DescriptionElementBase element) {

            this.element = element;

            if(element.isInstanceOf(CategoricalData.class)){

                CategoricalData elementData = (CategoricalData)element;

                elementData.getStatesOnly().forEach(state->stateUuids.add(state.getUuid()));

            }

            else if(element.isInstanceOf(QuantitativeData.class)){

                QuantitativeData elementData = (QuantitativeData)element;

                elementData.getStatisticalValues().forEach(value->{

                    if(value.getType().equals(StatisticalMeasure.AVERAGE())){

                        avgs.add(value.getValue());

                    }

                    else if(value.getType().equals(StatisticalMeasure.EXACT_VALUE())){

                        exacts.add(value.getValue());

                    }

                    else if(value.getType().equals(StatisticalMeasure.MAX())){

                        maxs.add(value.getValue());

                    }

                    else if(value.getType().equals(StatisticalMeasure.MIN())){

                        mins.add(value.getValue());

                    }

                    else if(value.getType().equals(StatisticalMeasure.SAMPLE_SIZE())){

                        sampleSizes.add(value.getValue());

                    }

                    else if(value.getType().equals(StatisticalMeasure.STANDARD_DEVIATION())){

                        standardDevs.add(value.getValue());

                    }

                    else if(value.getType().equals(StatisticalMeasure.TYPICAL_LOWER_BOUNDARY())){