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.eflora.centralAfrica.ericaceae;

import java.util.List;

import java.util.regex.Matcher;

import java.util.regex.Pattern;

import org.apache.log4j.Logger;

import org.jdom.Element;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.ext.ipni.IpniService;

import eu.etaxonomy.cdm.io.eflora.EfloraImportState;

import eu.etaxonomy.cdm.io.eflora.EfloraTaxonImport;

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

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.OriginalSourceType;

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.HomotypicalGroup;

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

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

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

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

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

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

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

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

/**

 * @author a.mueller

 *

 */

@Component

public class CentralAfricaEricaceaeTaxonImport  extends EfloraTaxonImport  {

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

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.eflora.EfloraTaxonImport#handleNomenclaturalReference(eu.etaxonomy.cdm.model.name.NonViralName, java.lang.String)

	 */

	@Override

	protected TeamOrPersonBase handleNomenclaturalReference(NonViralName name, String value) {

		Reference nomRef = ReferenceFactory.newGeneric();

		nomRef.setTitleCache(value, true);

		parseNomStatus(nomRef, name);

		name.setNomenclaturalReference(nomRef);

		String microReference = parseReferenceYearAndDetail(nomRef);

		microReference = removeTrailing(microReference, ")");

		microReference = parseHomonym(microReference, name);

		name.setNomenclaturalMicroReference(microReference);

		TeamOrPersonBase  nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class);

		TeamOrPersonBase  refTeam = nomRef.getAuthorship();

		if (nameTeam == null ){

			logger.warn("Name has nom. ref. but no author team. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value);

		}else if (refTeam == null ){

			logger.warn("Name has nom. ref. but no nom.ref. author. Name: " + name.getTitleCache() + ", Nom.Ref.: " + value);

		}else if (! authorTeamsMatch(refTeam, nameTeam)){

			logger.warn("Nom.Ref. author and comb. author do not match: " + nomRef.getTitleCache() + " <-> " + nameTeam.getNomenclaturalTitle());

		}else {

			nomRef.setAuthorship(nameTeam);

			nomRef.setTitle(CdmUtils.Nz(nomRef.getTitle()) + " - no title given yet -");

			nameTeam.setTitleCache(refTeam.getTitleCache(), true);

		}

		return nameTeam;

	}

	/**

	 * Extracts the date published part and returns micro reference

	 * @param ref

	 * @return

	 */

	protected String parseReferenceYearAndDetail(Reference ref){

		String detailResult = null;

		String titleToParse = ref.getTitleCache();

		titleToParse = removeReferenceBracket(titleToParse, ref);

		int detailStart = titleToParse.indexOf(":");

		if (detailStart >=  0){

			detailResult = titleToParse.substring(detailStart + 1);

			titleToParse = titleToParse.substring(0, titleToParse.length() -  detailResult.length() - 1).trim();

			detailResult = detailResult.trim();

		}

		String reYear = "\\s[1-2]{1}[0-9]{3}";

		String reYearPeriod = reYear;

//

//		//pattern for the whole string

		Pattern patReference = Pattern.compile( reYearPeriod );

		Matcher matcher = patReference.matcher(titleToParse);

		if (matcher.find()){

			int start = matcher.start();

			int end = matcher.end();

//

			String strPeriod = titleToParse.substring(start, end);

			TimePeriod datePublished = TimePeriodParser.parseString(strPeriod);

			ref.setDatePublished(datePublished);

			String author = titleToParse.substring(0, start).trim();

			author = parseInRefrence(ref, author);

			TeamOrPersonBase team = parseSingleTeam(author);

			ref.setAuthorship(team);

			ref.setProtectedTitleCache(false);

		}else{

			logger.warn("Could not parse reference: " +  titleToParse);

		}

		return detailResult;

	}

	private String parseInRefrence(Reference ref, String author) {

		int pos = author.indexOf(" in ");

		if (pos > -1){

			String inAuthorString = author.substring(pos + 4);

			String myAuthorString = author.substring(0, pos);

			Reference inReference = ReferenceFactory.newGeneric();

			TeamOrPersonBase inAuthor = parseSingleTeam(inAuthorString);

			inReference.setAuthorship(inAuthor);

			ref.setInReference(inReference);

			return myAuthorString;

		}else{

			return author;

		}

	}

	private String removeReferenceBracket(String refString, Reference ref) {

		String titleToParse = refString;

		String reBracket = "\\(.*\\).?";

		Pattern patBracket = Pattern.compile(reBracket);

		Matcher matcher = patBracket.matcher(titleToParse);

		if (matcher.matches()){

			int start = matcher.start() + 1;

			int end = matcher.end() -1 ;

			if (! titleToParse.endsWith("")){

				end = end - 1;

			}

			titleToParse = titleToParse.substring(start, end);

			ref.setTitleCache(titleToParse);

		}

		return titleToParse;

	}

	/**

	 * @param taxon

	 * @param name

	 * @param value

	 */

	@Override

	protected TeamOrPersonBase<?> handleNameUsage(Taxon taxon, NonViralName<?> name, String referenceTitle, TeamOrPersonBase lastTeam) {

		Reference ref = ReferenceFactory.newGeneric();

		ref.setTitleCache(referenceTitle, true);

		TeamOrPersonBase<?> team = getReferenceAuthor(ref, name);

		ref.setAuthorship(team);

		String[] multipleReferences = ref.getTitleCache().split("&");

		TaxonDescription description = getDescription(taxon);

		for (String singleReferenceString : multipleReferences){

			Reference singleRef = ReferenceFactory.newGeneric();

			singleRef.setTitleCache(singleReferenceString.trim(), true);

			singleRef.setAuthorship(team);

			String microReference = parseReferenceYearAndDetailForUsage(singleRef);

			singleRef.setTitle( CdmUtils.Nz(singleRef.getTitle()) + " - no title given yet -");

	//		parseReferenceType(ref);

			TextData textData = TextData.NewInstance(Feature.CITATION());

			textData.addSource(OriginalSourceType.PrimaryTaxonomicSource, null, null, singleRef, microReference, name, null);

			description.addElement(textData);

		}

		return team;

	}

	private String parseReferenceYearAndDetailForUsage(Reference ref) {

		String detailResult = null;

		String titleToParse = ref.getTitleCache().trim();

		int detailStart = titleToParse.indexOf(":");

		if (detailStart >=  0){

			detailResult = titleToParse.substring(detailStart + 1);

			titleToParse = titleToParse.substring(0, titleToParse.length() -  detailResult.length() - 1).trim();

			detailResult = detailResult.trim();

		}

		String reYear = "^[1-2]{1}[0-9]{3}[a-e]?$";

		String reYearPeriod = reYear;

//

//			//pattern for the whole string

		Pattern patReference = Pattern.compile( reYearPeriod );

		Matcher matcher = patReference.matcher(titleToParse);

		if (! matcher.find()){

			logger.warn("Could not parse year: " +  titleToParse);

		}else{

			if (Pattern.matches("^[1-2]{1}[0-9]{3}[a-e]$", titleToParse)){

				String title = titleToParse.substring(4,5);

				ref.setTitle(title);

				titleToParse = titleToParse.substring(0, 4);

			}

			ref.setProtectedTitleCache(false);

		}

		TimePeriod datePublished = TimePeriodParser.parseString(titleToParse);

		ref.setDatePublished(datePublished);

		return detailResult;

	}

	protected TeamOrPersonBase getReferenceAuthor (Reference ref, NonViralName name) {

		String titleString = ref.getTitleCache();

		String re = "\\(.*\\)";

		Pattern pattern = Pattern.compile(re);

		Matcher matcher = pattern.matcher(titleString);

		if (matcher.find()){

			int start = matcher.start();

			String authorString = titleString.substring(0, start).trim();

			String restString = titleString.substring(start + 1 , matcher.end() - 1);

			TeamOrPersonBase team = getAuthorTeam(authorString, name);

			ref.setTitleCache(restString, true);

			return team;

		}else{

			logger.warn("Title does not match: " + titleString);

			return null;

		}

	}

	private TeamOrPersonBase getAuthorTeam(String authorString, NonViralName name) {

		//TODO atomize

//		TeamOrPersonBase nameTeam = CdmBase.deproxy(name.getCombinationAuthorship(), TeamOrPersonBase.class);

//		String nameTeamTitle = nameTeam == null ? "" : nameTeam.getNomenclaturalTitle();

//		if (nameTeam == null || ! authorTeamsMatch(authorString, nameTeamTitle)){

//			logger.warn("Author teams do not match: " + authorString + " <-> " + nameTeamTitle);

			TeamOrPersonBase result = parseSingleTeam(authorString);

			result.setTitleCache(authorString, true);

			return result;

//		}else{

//			nameTeam.setTitleCache(authorString, true);

//			return nameTeam;

//		}

	}

	/**

	 * @param refAuthorTeam

	 * @param nameTeam

	 * @return

	 */

	private boolean authorTeamsMatch(TeamOrPersonBase refAuthorTeam, TeamOrPersonBase nameTeam) {

		String nameTeamString = nameTeam.getNomenclaturalTitle();

		String refAuthorTeamString = refAuthorTeam.getTitleCache();

		if (nameTeamString.equalsIgnoreCase(refAuthorTeamString)){

			return true;

		}

		if (nameTeamString.endsWith(".")){

			nameTeamString = nameTeamString.substring(0, nameTeamString.length() - 1 );

			if (refAuthorTeamString.startsWith(nameTeamString)){

				return true;

			}else{

				return checkSingleAndIpniAuthor(nameTeam, refAuthorTeam);

			}

		}else{

			if (nameTeamString.endsWith(refAuthorTeamString) || refAuthorTeamString.endsWith(nameTeamString)){

				return true;

			}else{

				return checkSingleAndIpniAuthor(nameTeam, refAuthorTeam);

			}

		}

	}

	private boolean checkSingleAndIpniAuthor(TeamOrPersonBase nameTeam, TeamOrPersonBase refAuthorTeam) {

		if ( nameTeam.isInstanceOf(Team.class) && ((Team)nameTeam).getTeamMembers().size()> 1 ||

				refAuthorTeam.isInstanceOf(Team.class) && ((Team)refAuthorTeam).getTeamMembers().size()> 1){

			//class

			if (! (nameTeam.isInstanceOf(Team.class) && refAuthorTeam.isInstanceOf(Team.class) ) ){

				logger.warn("Only one author is a real team");

				return false;

			}

			Team realNameTeam = (Team)nameTeam;

			Team realRefAuthorTeam = (Team)refAuthorTeam;

			//size

			if (realNameTeam.getTeamMembers().size() != realRefAuthorTeam.getTeamMembers().size()){

				logger.warn("Teams do not have the same size");

				return false;

			}

			//empty teams

			if (realNameTeam.getTeamMembers().size() == 0){

				logger.warn("Teams are empty");

				return false;

			}

			//compare each team member

			for (int i = 0; i < realNameTeam.getTeamMembers().size(); i++){

				Person namePerson = realNameTeam.getTeamMembers().get(i);

				Person refPerson = realRefAuthorTeam.getTeamMembers().get(i);

				if ( authorTeamsMatch(refPerson, namePerson) == false){

					return false;

				}

			}

			return true;

		}

		boolean result = checkIpniAuthor(nameTeam.getNomenclaturalTitle(), refAuthorTeam);

		return result;

	}

	private boolean checkIpniAuthor(String nameTeamString, TeamOrPersonBase refAuthorTeam) {

		IpniService ipniService = new IpniService();

		List<Person> ipniAuthors = ipniService.getAuthors(nameTeamString, null, null, null, null, null);

		if (ipniAuthors != null){

			for (Person ipniAuthor : ipniAuthors){

				if (ipniAuthor.getLastname() != null && ipniAuthor.getLastname().equalsIgnoreCase(refAuthorTeam.getTitleCache())){

					return true;

				}

				logger.warn(ipniAuthor.getTitleCache() + " <-> " + refAuthorTeam.getTitleCache());

			}

		}else{

			logger.warn("IPNI not available");

		}

		return false;

	}

	/**

	 * @param state

	 * @param elNom

	 * @param taxon

	 * @param homotypicalGroup

	 */

	@Override

	protected void handleTypeRef(EfloraImportState state, Element elNom, Taxon taxon, HomotypicalGroup homotypicalGroup) {

		verifyNoChildren(elNom);

		String typeRef = elNom.getTextNormalize();

		typeRef = removeStartingTypeRefMinus(typeRef);

		typeRef = removeTypePrefix(typeRef);

		TypeDesignationBase typeDesignation = SpecimenTypeDesignation.NewInstance();

		makeSpecimenTypeDesignation(new StringBuffer("Type"), typeRef, typeDesignation);

		for (TaxonNameBase name : homotypicalGroup.getTypifiedNames()){

			name.addTypeDesignation(typeDesignation, true);

		}

	}

	private String removeTypePrefix(String typeRef) {

		typeRef = typeRef.trim().replace("Type: ", "").replace("Types: ", "").trim();

		return typeRef;

	}

	@Override

    protected void handleGenus(String value, TaxonNameBase taxonName) {

		// do nothing

	}

}