EDIT

// $Id$

/**

* 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.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

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

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

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

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.NonViralName;

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

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

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

/**

 * @author a.mueller

 * @date 22.11.2011

 *

 */

	private static final String CORE_ID = "coreId";

	/**

	 * @param state

	 */

	}

	public IReader<MappedCdmBase> map(CsvStreamItem item ){

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

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

		String id = getSourceId(item);

		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);

		//author

		//date

		TimePeriod publicationDate = handleDate(strDate);

		reference.setDatePublished(publicationDate);

		//title

		reference.setTitle(strTitle);

		//inreference

			reference.setInReference(inRef);

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

		//URI

		handleIdentifier(strIdentifier, reference);

		//type

		return new ListReader<MappedCdmBase>(resultList);

	}

		//guess a nom ref

		if (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 != null && taxon.getName() != null && reference != null && taxon.getName().isInstanceOf(NonViralName.class)){

				boolean isNomRef = false;

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

				Integer combYear = null;

				Integer origYear = null;

				if (nvn.isInstanceOf(ZoologicalName.class)){

					ZoologicalName zooName = CdmBase.deproxy(nvn, ZoologicalName.class);

					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()){

				String message = "Reference entry does not belong to an existing taxon. Reference type can not be determined!";

				fireWarningEvent(message,item, 4);

				//do nothing

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

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

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

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

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

				for (Taxon tax: syn.getAcceptedTaxa()){

					TaxonDescription desc = getTaxonDescription(tax, false);

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

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

				}

			}

		}

	}

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

		Feature feature = Feature.CITATION();

		TextData textData = TextData.NewInstance(feature);

		DescriptionElementSource source = DescriptionElementSource.NewInstance(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 = TimePeriod.parseString(strDate);

		return tp;

	}

	private TeamOrPersonBase handleCreator(String strCreator) {

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

		return team;

	}

	public String getSourceId(CsvStreamItem item) {

		String id = item.get(CORE_ID);

		return id;

	}

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

	@Override

	protected void makeForeignKeysForItem(CsvStreamItem 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();

	}

}