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 org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;

import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;

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.agent.Institution;

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

import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;

import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;

import eu.etaxonomy.cdm.model.name.TaxonName;

import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;

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

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

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

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

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

/**

 * @author a.mueller

 * @since 22.11.2011

 *

 */

public class GbifTypesAndSpecimen2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>

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

	@SuppressWarnings("unused")

	private static final Logger logger = LogManager.getLogger(GbifTypesAndSpecimen2CdmConverter.class);

	private static final String CORE_ID = "coreId";

	/**

	 * @param state

	 */

	public GbifTypesAndSpecimen2CdmConverter(DwcaDataImportStateBase state) {

		super(state);

	}

	@Override

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

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

		Reference sourceReference = state.getTransactionalSourceReference();

		String sourceReferecenDetail = null;

		String id = getSourceId(item);

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

		if (taxon != null){

			String typeStatusStr = item.get(TermUri.DWC_TYPE_STATUS);

			boolean isType = false;

			TypeDesignationStatusBase<?> typeStatus = null;

			if ( ! isNoTypeStatus(typeStatusStr)){

				isType = true;

				typeStatus = getTypeStatus(typeStatusStr, item);

			}

			SpecimenOrObservationType unitType = SpecimenOrObservationType.DerivedUnit;

			if (hasDerivedUnit(item, isType)){

				unitType = SpecimenOrObservationType.PreservedSpecimen;

			}else{

				unitType = SpecimenOrObservationType.FieldUnit;

			}

			DerivedUnitFacade facade = DerivedUnitFacade.NewInstance(unitType);

			String catalogNumber = item.get(TermUri.DWC_CATALOG_NUMBER);

			Collection collection = getCollection(state, item, resultList);

			facade.setCollection(collection);

			facade.setCatalogNumber(catalogNumber);

			DerivedUnit specimen = facade.innerDerivedUnit();

			if (isType){

				TaxonName name = taxon.getName();

				if (typeStatus.isInstanceOf(SpecimenTypeDesignationStatus.class)){

					SpecimenTypeDesignationStatus status = CdmBase.deproxy(typeStatus, SpecimenTypeDesignationStatus.class);

					name.addSpecimenTypeDesignation(specimen, status, null, null, null, false, true);

					MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(taxon);

					resultList.add(mcb);

				}else if (typeStatus.isInstanceOf(NameTypeDesignationStatus.class)){

					String message = "NameTypeDesignation not yet implemented";

					fireWarningEvent(message, item, 8);

				}else{

					String message = "Undefined type status: %s";

					message = String.format(message, typeStatus);

					fireWarningEvent(message, item, 8);

				}

			}

			MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(specimen);

			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);

	}

	private Collection getCollection(DwcaDataImportStateBase state, StreamItem item,

	        List<MappedCdmBase<? extends CdmBase>> resultList) {

		String institutionCode = item.get(TermUri.DWC_INSTITUTION_CODE);

		String collectionCode = item.get(TermUri.DWC_COLLECTION_CODE);

		//institution

		Institution institution = getInstitutionByInstitutionCode(item, institutionCode);

		if (institution != null){

			MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(item.term, item.get(TermUri.DWC_INSTITUTION_CODE), institution);

			resultList.add(mcb);

		}

		//collection

		Collection collection = getCollectionByCollectionCode(item, collectionCode, institution);

		if (collection != null){

			MappedCdmBase<? extends CdmBase>  mcb = new MappedCdmBase<>(item.term, item.get(TermUri.DWC_COLLECTION_CODE), collection);

			resultList.add(mcb);

		}

		return collection;

	}

	private Collection getCollectionByCollectionCode(StreamItem item, String collectionCode, Institution institution) {

		String namespace = TermUri.DWC_COLLECTION_CODE.toString();

		List<Collection> result = state.get(namespace, collectionCode, Collection.class);

		if (result.isEmpty()){

			return makeNewCollection(collectionCode, institution);

		}else if (result.size() == 1){

			return result.iterator().next();

		}else {

			int equalInstitutes = 0;

			Collection lastEqualInstituteCollection = null;

			String collectionInstitutionCode = makeCollectionInstitutionCode(collectionCode, institution);

			for (Collection collection: result){

				String collectionInstitutionCode2 = makeCollectionInstitutionCode(collection.getCode() ,institution);

				if (collectionInstitutionCode.equals(collectionInstitutionCode2)){

					equalInstitutes++;

					lastEqualInstituteCollection = collection;

				}

			}

			if(equalInstitutes == 0){

				return makeNewCollection(collectionCode, institution);

			}else{

				if (equalInstitutes > 1){

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

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

				}

				return lastEqualInstituteCollection;

			}

		}

	}

	/**

	 * @param collectionCode

	 * @param institution

	 */

	private String makeCollectionInstitutionCode(String collectionCode, Institution institution) {

		String collectionInstitutionCode = collectionCode + "@" + institution == null ? "NULL" : institution.getCode();

		return collectionInstitutionCode;

	}

	/**

	 * @param collectionCode

	 * @param institution

	 * @return

	 */

	private Collection makeNewCollection(String collectionCode,

			Institution institution) {

		//try to find in cdm

		Collection newCollection = Collection.NewInstance();

		newCollection.setCode(collectionCode);

		newCollection.setInstitute(institution);

		return newCollection;

	}

	private Institution getInstitutionByInstitutionCode(StreamItem item, String institutionCode) {

		String namespace = TermUri.DWC_COLLECTION_CODE.toString();

		List<Institution> result = state.get(namespace, institutionCode, Institution.class);

		if (result.isEmpty()){

			//try to find in cdm

			Institution newInstitution = Institution.NewInstance();

			newInstitution.setCode(institutionCode);

			return newInstitution;

		}

		if (result.size() > 1){

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

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

		}

		return result.iterator().next();

	}

	private boolean hasDerivedUnit(StreamItem item, boolean isType) {

		return isNotBlank(item.get(TermUri.DWC_INSTITUTION_CODE)) ||

				isNotBlank(item.get(TermUri.DWC_COLLECTION_CODE)) ||

				isNotBlank(item.get(TermUri.DWC_CATALOG_NUMBER))||

				isType;

		//TO BE CONTINUED

	}

	private boolean isNoTypeStatus(String typeStatus) {

		if (isBlank(typeStatus)){

			return true;

		}else if (typeStatus.equalsIgnoreCase("Nontype")){   //eMonocats Scratchpads

			return true;

		}else{

			return false;

		}

	}

	/**

	 * Returns the type designation. Should never return null

	 * except for blank typeStatus.

	 * @param typeStatus

	 * @param item

	 * @return

	 */

	private TypeDesignationStatusBase<?> getTypeStatus(String typeStatus, StreamItem item) {

		//TODO move to transformer or handle somehow different (e.g. transformer for http://vocabularies.gbif.org/vocabularies/type_status )

		//preliminary implementation for those types needed for eMonocots import

		if (isBlank(typeStatus)){

			return null;

		}else if (typeStatus.matches("(?i)holotype")){

			return SpecimenTypeDesignationStatus.HOLOTYPE();

		}else if (typeStatus.matches("(?i)syntype")){

			return SpecimenTypeDesignationStatus.SYNTYPE();

		}else{

			String message = "Type status not recognized: %s";

			message = String.format(message, typeStatus);

			fireWarningEvent(message, item, 12);

			return SpecimenTypeDesignationStatus.TYPE();

		}

	}

	@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);

		}

		//collection code

		TermUri uri = TermUri.DWC_COLLECTION_CODE;

		String valueStr = item.get(uri);

		if ( hasValue(value = valueStr)){

			key = uri.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());

 		return result;

	}

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

	@Override

	public String toString(){

		return this.getClass().getName();

	}

}