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.net.URI;

import java.util.ArrayList;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import com.ibm.lsid.MalformedLSIDException;

import eu.etaxonomy.cdm.io.dwca.TermUri;

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

import eu.etaxonomy.cdm.model.agent.Team;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;

/**

 * @author a.mueller

 * @date 22.11.2011

 *

 */

public class GbifReferenceCsv2CdmConverter extends PartitionableConverterBase<DwcaDataImportConfiguratorBase, DwcaDataImportStateBase<DwcaDataImportConfiguratorBase>>

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

	private static final Logger logger = Logger.getLogger(GbifReferenceCsv2CdmConverter.class);

	private static final String CORE_ID = "coreId";

	/**

	 * @param state

	 */

	public GbifReferenceCsv2CdmConverter(DwcaDataImportStateBase state) {

		super(state);

	}

	@Override

    public IReader<MappedCdmBase> map(StreamItem item ){

		List<MappedCdmBase> resultList = new ArrayList<MappedCdmBase>();

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

		Reference sourceReference = state.getTransactionalSourceReference();

		String sourceReferecenDetail = null;

		String id = getSourceId(item);

		TaxonBase<?> taxon = getTaxonBase(id, item, TaxonBase.class, state);

		if (isNotBlank(id) && taxon == null){

			String message = "Taxon for id %s could not be found";

			message = String.format(message, id);

			fireWarningEvent(message, item, 8);

		}

		String strCreator = getValue(item, TermUri.DC_CREATOR);

		String strDate = getValue(item, TermUri.DC_DATE);

		String strTitle = getValue(item, TermUri.DC_TITLE);

		String strSource = getValue(item, TermUri.DC_SOURCE);

		String strIdentifier = getValue(item, TermUri.DC_IDENTIFIER);

		String strType = getValue(item, TermUri.DC_TYPE);

		Reference reference = ReferenceFactory.newGeneric();

		resultList.add(new MappedCdmBase<CdmBase>(reference));

		//author

		TeamOrPersonBase<?> author = handleCreator(strCreator);

		reference.setAuthorship(author);

		//date

		TimePeriod publicationDate = handleDate(strDate);

		reference.setDatePublished(publicationDate);

		//title

		reference.setTitle(strTitle);

		//inreference

		Reference inRef = handleInRef(strSource);

		if (inRef != null){

			reference.setInReference(inRef);

			resultList.add(new MappedCdmBase<CdmBase>(inRef));

		}

		//URI

		handleIdentifier(strIdentifier, reference);

		//type

		handleType(reference, strType, taxon, resultList, item);

		return new ListReader<MappedCdmBase>(resultList);

	}

	private void handleType(Reference reference, String strType, TaxonBase<?> taxon, List<MappedCdmBase> resultList, StreamItem item) {

		// TODO handleType not yet implemented

		if (taxon == null){

			String message = "Taxon is null. Reference not imported.";

			fireWarningEvent(message,item, 4);

			//do nothing

		}else{

			boolean isNomRef = false;

			if (isNotBlank(strType)){

				if (strType.matches("Botanical Protologue")){

					if (taxon.getName() != null && reference != null && taxon.getName().isNonViral()){

						INonViralName nvn = taxon.getName();

						nvn.setNomenclaturalReference(reference);

						isNomRef = true;

					}else{

						//TODO

					}

				}

			}

			//guess a nom ref

			if (isNomRef == false && config.isGuessNomenclaturalReferences()){

				//if reference equals in author and year we assume that it is the nom ref

				//this information is usually only available for ICZN names

				if (taxon.getName() != null && reference != null && taxon.getName().isNonViral()){

					INonViralName nvn = taxon.getName();

					String taxonAuthor = nvn.getAuthorshipCache();

					String refAuthor = reference.getAuthorship().getNomenclaturalTitle();

					Integer combYear = null;

					Integer origYear = null;

					if (nvn.isZoological()){

						IZoologicalName zooName = (IZoologicalName)CdmBase.deproxy(nvn);

						combYear = zooName.getPublicationYear();

						origYear = zooName.getOriginalPublicationYear();

					}

					String refYear = reference.getYear();

					//combination compare

					if (taxonAuthor != null && taxonAuthor.equals(refAuthor)){

						if (combYear != null && String.valueOf(combYear).equals(refYear)){

							//is nom Ref

							isNomRef = true;

							nvn.setNomenclaturalReference(reference);

						}else if (origYear != null && String.valueOf(origYear).equals(refYear)){

							//TODO not yet handled by CDM

						}

					}

				}

			}

			if (config.isHandleAllRefsAsCitation()){

				if (taxon.isInstanceOf(Taxon.class)){

					TaxonDescription desc = getTaxonDescription(CdmBase.deproxy(taxon, Taxon.class), false);

					createCitation(desc, reference, taxon.getName());

					resultList.add(new MappedCdmBase<CdmBase>(desc));

				}else if (taxon.isInstanceOf(Synonym.class)){

					Synonym syn = CdmBase.deproxy(taxon, Synonym.class);

					Taxon tax = syn.getAcceptedTaxon();

					if (tax != null){

    					TaxonDescription desc = getTaxonDescription(tax, false);

    					createCitation(desc, reference, syn.getName());

    					resultList.add(new MappedCdmBase<CdmBase>(desc));

					}

				}

			}

		}

	}

	private void createCitation(TaxonDescription desc, Reference ref, TaxonName nameUsedInSource) {

		Feature feature = Feature.CITATION();

		TextData textData = TextData.NewInstance(feature);

		DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(ref, null, nameUsedInSource, null);

		textData.addSource(source);

		desc.addElement(textData);

	}

	private void handleIdentifier(String strIdentifier, Reference reference) {

		if (StringUtils.isBlank(strIdentifier)){

			return;

		}else if (LSID.isLsid(strIdentifier)){

			LSID lsid;

			try {

				lsid = new LSID(strIdentifier);

				reference.setLsid(lsid);

			} catch (MalformedLSIDException e) {

				//TODO should not happen as we have checked before

				throw new RuntimeException(e);

			}

		}

		try {

			URI uri = URI.create(strIdentifier);

			reference.setUri(uri);

		} catch (Exception e) {

			logger.debug("Reference is not an URI");

		}

		//TODO further identifier types

	}

	private Reference handleInRef(String strSource) {

		if (StringUtils.isBlank(strSource)){

			return null;

		}else{

			Reference inRef = ReferenceFactory.newGeneric();

			return inRef;

		}

	}

	private TimePeriod handleDate(String strDate) {

		TimePeriod tp = TimePeriodParser.parseString(strDate);

		return tp;

	}

	private TeamOrPersonBase handleCreator(String strCreator) {

		Team team = Team.NewTitledInstance(strCreator, strCreator);

		return team;

	}

	@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;

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

			key = TermUri.DWC_TAXON.toString();

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

			keySet.add(value);

		}

	}

	@Override

	public Set<String> requiredSourceNamespaces() {

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

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

 		return result;

	}

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

	@Override

	public String toString(){

		return this.getClass().getName();

	}

}