EDIT

/**

* Copyright (C) 2009 EDIT

* European Distributed Institute of Taxonomy

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

*

* The contents of this file are subject to the Mozilla Public License Version 1.1

* See LICENSE.TXT at the top of this package for the full license terms.

*/

package eu.etaxonomy.cdm.io.dwca.in;

import java.util.ArrayList;

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 eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

import eu.etaxonomy.cdm.io.stream.IPartitionableConverter;

import eu.etaxonomy.cdm.io.stream.IReader;

import eu.etaxonomy.cdm.io.stream.ListReader;

import eu.etaxonomy.cdm.io.stream.MappedCdmBase;

import eu.etaxonomy.cdm.io.stream.PartitionableConverterBase;

import eu.etaxonomy.cdm.io.stream.StreamItem;

import eu.etaxonomy.cdm.io.stream.terms.TermUri;

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

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

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

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

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

import eu.etaxonomy.cdm.model.reference.Reference;

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

import eu.etaxonomy.cdm.model.term.TermVocabulary;

/**

 * @author a.mueller

 * @since 22.11.2011

 *

 */

public class GbifDistributionCsv2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>

						implements IPartitionableConverter<StreamItem, IReader<CdmBase>, String>{

	@SuppressWarnings("unused")

	private static final Logger logger = Logger.getLogger(GbifDistributionCsv2CdmConverter.class);

	private static final String CORE_ID = "coreId";

	/**

	 * @param state

	 */

	public GbifDistributionCsv2CdmConverter(DwcaDataImportStateBase state) {

		super(state);

	}

	@Override

    public IReader<MappedCdmBase<? extends CdmBase>> map(StreamItem item ){

		List<MappedCdmBase<? extends CdmBase>> resultList = new ArrayList<>();

		Map<String, String> csv = item.map;

		Reference sourceReference = state.getTransactionalSourceReference();

		String sourceReferecenDetail = null;

		String id = getSourceId(item);

		Taxon taxon = getTaxonBase(id, item, Taxon.class, state);

		if (taxon != null){

		    //area

		    String locality = item.get(TermUri.DWC_LOCALITY);

			String locationId = item.get(TermUri.DWC_LOCATION_ID);

			NamedArea area = getAreaByLocationId(item, locationId, locality, resultList);

			if (area != null){

				MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(TermUri.DWC_LOCATION_ID, csv.get(TermUri.DWC_LOCATION_ID.toString()), area);

				resultList.add(mcb);

			}else if (! config.isExcludeLocality()){

				area = getAreaByLocality(item, locality);

				MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(TermUri.DWC_LOCALITY, csv.get(TermUri.DWC_LOCALITY.toString()), area);

				resultList.add(mcb);

			}

			//status

			String establishmentMeans = item.get(TermUri.DWC_ESTABLISHMENT_MEANS);

	        String occurrenceStatus = item.get(TermUri.DWC_OCCURRENCE_STATUS);

			PresenceAbsenceTerm status = getPresenceAbsenceStatus(item, establishmentMeans, occurrenceStatus, resultList);

			if (area != null){

				TaxonDescription desc = getTaxonDescription(taxon, false);

				Distribution distribution = Distribution.NewInstance(area, status);

				desc.addElement(distribution);

				//save taxon

				MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(item.term, csv.get(CORE_ID.toString()), taxon);

				resultList.add(mcb);

			}

		}else{

			String message = "Can't retrieve taxon from database for id '%s'";

			fireWarningEvent(String.format(message, id), item, 12);

		}

		//return

		return new ListReader<>(resultList);

	}

	/**

     * @param item

	 * @param occurrenceStatus

	 * @param establishmentMeans

     * @param resultList

     * @return

     */

    private PresenceAbsenceTerm getPresenceAbsenceStatus(StreamItem item,

            String establishmentMeans, String occurrenceStatus, List<MappedCdmBase<? extends CdmBase>> resultList) {

        PresenceAbsenceTerm status = null;

        if (isBlank(establishmentMeans) && isBlank(occurrenceStatus)){

            status = PresenceAbsenceTerm.PRESENT();

        }else{

            String statusStr = CdmUtils.concat(" - ", occurrenceStatus, establishmentMeans);

            String namespace = PresenceAbsenceTerm.class.getCanonicalName();

            List<PresenceAbsenceTerm> result = state.get(namespace, statusStr, PresenceAbsenceTerm.class);

            try{

                if (result.isEmpty()){

                    PresenceAbsenceTerm newStatus = state.getTransformer().getPresenceTermByKey(statusStr);

                    if (newStatus != null){

                        return newStatus;

                    }

                    //try to find in cdm

                    newStatus = getExistingPresenceAbsenceTerm(statusStr);

                    if (newStatus != null){

                        return newStatus;

                    }

                    UUID statusUuid = state.getTransformer().getPresenceTermUuid(statusStr);

                    newStatus = state.getCurrentIO().getPresenceTerm(state, statusUuid, statusStr, statusStr, null, false);

                    //should not happen

                    if (newStatus == null){

                        newStatus = PresenceAbsenceTerm.NewPresenceInstance(statusStr, statusStr, statusStr);

                        state.getCurrentIO().saveNewTerm(newStatus);

                        MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(namespace, statusStr, newStatus);

                        resultList.add(mcb);

                    }

                    state.putMapping(namespace, statusStr, newStatus);

                    return newStatus;

                }

                if (result.size() > 1){

                    String message = "There is more than 1 cdm entity matching given occurrence status/establishment means '%s'."

                            + " I take an arbitrary one.";

                    fireWarningEvent(String.format(message, statusStr), item, 4);

                }

                return result.iterator().next();

            } catch (UndefinedTransformerMethodException e) {

                String message = "GetNamedArea not yet supported by DwcA-Transformer. This should not have happend. Please contact your application developer.";

                fireWarningEvent(message, item, 8);

                return null;

            }

        }

        return status;

    }

    /**

     * @param statusStr

     * @return

     */

    private PresenceAbsenceTerm getExistingPresenceAbsenceTerm(String statusStr) {

        TermVocabulary<PresenceAbsenceTerm> voc = PresenceAbsenceTerm.PRESENT().getVocabulary();

        for (PresenceAbsenceTerm status: voc.getTerms()){

            if (statusStr.equalsIgnoreCase(status.getLabel())){

                return status;

            }

        }

        return null;

    }

    private NamedArea getAreaByLocality(StreamItem item, String locality) {

		String namespace = TermUri.DWC_LOCALITY.toString();

		List<NamedArea> result = state.get(namespace, locality, NamedArea.class);

		if (result.isEmpty()){

			NamedArea newArea = NamedArea.NewInstance(locality, locality, locality);

			newArea.setTitleCache(locality, true);

			return newArea;

		}

		if (result.size() > 1){

			String message = "There is more than 1 cdm entity matching given locality '%s'. I take an arbitrary one.";

			fireWarningEvent(String.format(message, locality), item, 4);

		}

		return result.iterator().next();

	}

	private NamedArea getAreaByLocationId(StreamItem item, String locationId, String newLabel, List<MappedCdmBase<? extends CdmBase>> resultList) {

		String namespace = TermUri.DWC_LOCATION_ID.toString();

		if (isBlank(locationId)){

		    return null;

		}

		List<NamedArea> result = state.get(namespace, locationId, NamedArea.class);

		try{

    		if (result.isEmpty()){

    		    NamedArea newArea = state.getTransformer().getNamedAreaByKey(locationId);

    		    if (newArea != null){

                    return newArea;

                }

    		  //try to find in cdm

                newArea = getTdwgArea(locationId);

                if (newArea != null){

                    return newArea;

                }

    		    String label = isNotBlank(newLabel)? newLabel : locationId;

    		    UUID namedAreaUuid = state.getTransformer().getNamedAreaUuid(locationId);

    		    newArea = state.getCurrentIO().getNamedArea(state, namedAreaUuid, label, label, locationId, null);

    		    //should not happen

    		    if (newArea == null){

    		        newArea = NamedArea.NewInstance(label, label, locationId);

    //            state.putMapping(namespace, type, newArea);

                    state.getCurrentIO().saveNewTerm(newArea);

                    MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(namespace, locationId, newArea);

                    resultList.add(mcb);

                }

    			state.putMapping(namespace, locationId, newArea);

    			return newArea;

    		}

    		if (result.size() > 1){

    			String message = "There is more than 1 cdm entity matching given locationId '%s'. I take an arbitrary one.";

    			fireWarningEvent(String.format(message, locationId), item, 4);

    		}

    		return result.iterator().next();

        } catch (UndefinedTransformerMethodException e) {

            String message = "GetNamedArea not yet supported by DwcA-Transformer. This should not have happend. Please contact your application developer.";

            fireWarningEvent(message, item, 8);

            return null;

        }

	}

    /**

     * @param locationId

     * @return

     */

    protected NamedArea getTdwgArea(String locationId) {

        if (locationId == null){

            return null;

        }else if (locationId.startsWith("TDWG:")){

            locationId = locationId.substring("TDWG:".length()); //CoL case

        }

        return TdwgAreaProvider.getAreaByTdwgAbbreviation(locationId);

    }

	@Override

	public String getSourceId(StreamItem item) {

		String id = item.get(CORE_ID);

		return id;

	}

//********************** PARTITIONABLE **************************************/

	@Override

	protected void makeForeignKeysForItem(StreamItem item, Map<String, Set<String>> fkMap) {

		String value;

		String key;

		//taxon

		if ( hasValue(value = item.get(CORE_ID))){

			key = TermUri.DWC_TAXON.toString();

			Set<String> keySet = getKeySet(key, fkMap);

			keySet.add(value);

		}

		//areaId

		String locationId = item.get(TermUri.DWC_LOCATION_ID);

		if ( hasValue(value = locationId)){

			key = TermUri.DWC_LOCATION_ID.toString();

			Set<String> keySet = getKeySet(key, fkMap);

			keySet.add(value);

		}

	}

	@Override

	public Set<String> requiredSourceNamespaces() {

		Set<String> result = new HashSet<>();

 		result.add(TermUri.DWC_TAXON.toString());

 		result.add(TermUri.DWC_LOCATION_ID.toString());

 		result.add(TermUri.DWC_LOCALITY.toString());

 		return result;

	}

//******************* TO STRING ******************************************/

	@Override

	public String toString(){

		return this.getClass().getName();

	}

}