EDIT

/**

* Copyright (C) 2007 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.berlinModel.in;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.commons.lang.StringUtils;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

import eu.etaxonomy.cdm.database.update.DatabaseTypeNotSupportedException;

import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;

import eu.etaxonomy.cdm.io.berlinModel.in.validation.BerlinModelTaxonNameImportValidator;

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

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

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

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

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

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.Extension;

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;

/**

 * @author a.mueller

 * @created 20.03.2008

 */

@Component

public class BerlinModelTaxonNameImport extends BerlinModelImportBase {

    private static final long serialVersionUID = -8860800694286602016L;

    private static final boolean BLANK_TO_NULL = true;

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

	public static final String NAMESPACE = "TaxonName";

	public static final UUID SOURCE_ACC_UUID = UUID.fromString("c3959b4f-d876-4b7a-a739-9260f4cafd1c");

	private static int modCount = 5000;

	private static final String pluralString = "TaxonNames";

	private static final String dbTableName = "Name";

	public BerlinModelTaxonNameImport(){

		super(dbTableName, pluralString);

	}

	@Override

	protected String getIdQuery(BerlinModelImportState state) {

		if (state.getConfig().getNameIdTable()==null ){

			return super.getIdQuery(state);

		}else{

			return "SELECT nameId FROM " + state.getConfig().getNameIdTable() + "";

		}

	}

	@Override

	protected String getRecordQuery(BerlinModelImportConfigurator config) {

		Source source = config.getSource();

			String facultativCols = "";

			String strFacTable = "RefDetail";

			String strFacColumn = "IdInSource";

			String strColAlias = null;

			if (checkSqlServerColumnExists(source, strFacTable, strFacColumn)){

				facultativCols +=  ", " + strFacTable + "." + strFacColumn ;

				if (! CdmUtils.Nz(strColAlias).equals("") ){

					facultativCols += " AS " + strColAlias;

				}

			}

		String strRecordQuery =

					"SELECT Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +

                      		" RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +

                      		" RefDetail.SecondarySources, Rank.RankAbbrev, Rank.Rank " +

                      		facultativCols +

                    " FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND  " +

                    	" Name.NomRefFk = RefDetail.RefFk " +

                    	" LEFT OUTER JOIN Rank ON Name.RankFk = Rank.rankID " +

                " WHERE name.nameId IN ("+ID_LIST_TOKEN+") ";

					//strQuery += " AND RefDetail.PreliminaryFlag = 1 ";

					//strQuery += " AND Name.Created_When > '03.03.2004' ";

		return strRecordQuery +  "";

	}

	@Override

	protected void doInvoke(BerlinModelImportState state) {

		//update rank labels if necessary

		String strAbbrev = state.getConfig().getInfrGenericRankAbbrev();

		Rank rank = Rank.INFRAGENERICTAXON();

		testRankAbbrev(strAbbrev, rank);

		strAbbrev = state.getConfig().getInfrSpecificRankAbbrev();

		rank = Rank.INFRASPECIFICTAXON();

		testRankAbbrev(strAbbrev, rank);

		super.doInvoke(state);

	}

	private void testRankAbbrev(String strAbbrev, Rank rank) {

		if (strAbbrev != null){

			Representation rep = rank.getRepresentation(Language.ENGLISH());

			rep.setAbbreviatedLabel(strAbbrev);

			getTermService().saveOrUpdate(rank);

		}

	}

	@Override

	public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState state) {

		String dbAttrName;

		String cdmAttrName;

		boolean success = true ;

		BerlinModelImportConfigurator config = state.getConfig();

		Set<TaxonName> namesToSave = new HashSet<>();

		Map<String, Team> teamMap = partitioner.getObjectMap(BerlinModelAuthorTeamImport.NAMESPACE);

		ResultSet rs = partitioner.getResultSet();

		try {

			int i = 0;

			//for each reference

			while (rs.next()){

				if ((i++ % modCount) == 0 && i != 1 ){ logger.info("Names handled: " + (i-1));}

				//create TaxonName element

				int nameId = rs.getInt("nameId");

				Object authorFk = rs.getObject("AuthorTeamFk");

				Object exAuthorFk = rs.getObject("ExAuthorTeamFk");

				Object basAuthorFk = rs.getObject("BasAuthorTeamFk");

				Object exBasAuthorFk = rs.getObject("ExBasAuthorTeamFk");

				String strCultivarGroupName = rs.getString("CultivarGroupName");

				String strCultivarName = rs.getString("CultivarName");

				String nameCache = rs.getString("NameCache");

				String fullNameCache = rs.getString("FullNameCache");

				String uuid = null;

				if (resultSetHasColumn(rs,"UUID")){

					uuid = rs.getString("UUID");

				}

				try {

					//define rank

					boolean useUnknownRank = true;

					Rank rank = BerlinModelTransformer.rankId2Rank(rs, useUnknownRank, config.isSwitchSpeciesGroup());

					boolean allowInfraSpecTaxonRank = state.getConfig().isAllowInfraSpecTaxonRank() ;

					if (rank == null || rank.equals(Rank.UNKNOWN_RANK()) || (rank.equals(Rank.INFRASPECIFICTAXON()) && ! allowInfraSpecTaxonRank)){

						rank = handleProlesAndRaceSublusus(state, rs, rank);

					}

					if (rank.getId() == 0){

						getTermService().save(rank);

						logger.warn("Rank did not yet exist: " +  rank.getTitleCache());

					}

					//create TaxonName

					TaxonName<?,?> taxonName;

					if (config.getNomenclaturalCode() != null){

						taxonName = config.getNomenclaturalCode().getNewTaxonNameInstance(rank);

						//check cultivar

						if (taxonName.isBotanical()){

							if (isNotBlank(strCultivarGroupName) && isNotBlank(strCultivarName)){

								taxonName = TaxonNameFactory.NewCultivarInstance(rank);

							}

						}

					}else{

						taxonName = TaxonNameFactory.NewNonViralInstance(rank);

					}

					if (uuid != null){

						taxonName.setUuid(UUID.fromString(uuid));

					}

					if (rank == null){

						//TODO rank should never be null or a more sophisticated algorithm has to be implemented for genus/supraGenericName

						logger.warn("Rank is null. Genus epethiton was imported. May be wrong");

						success = false;

					}

					//epithets

					if (rank != null && rank.isSupraGeneric()){

						dbAttrName = "supraGenericName";

					}else{

						dbAttrName = "genus";

					}

					cdmAttrName = "genusOrUninomial";

					success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);

					dbAttrName = "genusSubdivisionEpi";

					cdmAttrName = "infraGenericEpithet";

					success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);

					dbAttrName = "speciesEpi";

					cdmAttrName = "specificEpithet";

					success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);

					dbAttrName = "infraSpeciesEpi";

					cdmAttrName = "infraSpecificEpithet";

					success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);

					dbAttrName = "unnamedNamePhrase";

					cdmAttrName = "appendedPhrase";

					success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);

					//Details

					dbAttrName = "details";

					cdmAttrName = "nomenclaturalMicroReference";

					success &= ImportHelper.addStringValue(rs, taxonName, dbAttrName, cdmAttrName, BLANK_TO_NULL);

					//nomRef

					success &= makeNomenclaturalReference(config, taxonName, nameId, rs, partitioner);

					//Source_Acc

					boolean colExists = true;

					try {

						colExists = state.getConfig().getSource().checkColumnExists("Name", "Source_Acc");

					} catch (DatabaseTypeNotSupportedException e) {

						logger.debug("Source does not support 'checkColumnExists'");

					}

					if (colExists){

						String sourceAcc = rs.getString("Source_Acc");

						if (StringUtils.isNotBlank(sourceAcc)){

							ExtensionType sourceAccExtensionType = getExtensionType(state, SOURCE_ACC_UUID, "Source_Acc","Source_Acc","Source_Acc");

							Extension datesExtension = Extension.NewInstance(taxonName, sourceAcc, sourceAccExtensionType);

						}

					}

					//created, notes

					boolean excludeUpdated = true;

					success &= doIdCreatedUpdatedNotes(state, taxonName, rs, nameId, NAMESPACE, excludeUpdated, false);

					//NonViralName

					if (taxonName.isNonViral()){

						INonViralName nonViralName = taxonName;

						//authorTeams

						if (teamMap != null ){

							nonViralName.setCombinationAuthorship(getAuthorTeam(teamMap, authorFk, nameId, config));

							nonViralName.setExCombinationAuthorship(getAuthorTeam(teamMap, exAuthorFk, nameId, config));

							nonViralName.setBasionymAuthorship(getAuthorTeam(teamMap, basAuthorFk, nameId, config));

							nonViralName.setExBasionymAuthorship(getAuthorTeam(teamMap, exBasAuthorFk, nameId, config));

						}else{

							logger.warn("TeamMap is null");

							success = false;

						}

					}//nonviralName

					//zoologicalName

					if (taxonName.isZoological()){

						IZoologicalName zooName = taxonName;

						makeZoologialName(rs, zooName, nameId);

					}

					//botanicalName

					else if (taxonName.isBotanical()){

						IBotanicalName botName = taxonName;

						success &= makeBotanicalNamePart(rs, botName) ;

					}

	//				dbAttrName = "preliminaryFlag";

					Boolean preliminaryFlag = rs.getBoolean("PreliminaryFlag");

					Boolean hybridFormulaFlag = rs.getBoolean("HybridFormulaFlag");  //hybrid flag does not lead to cache update in Berlin Model

					if (preliminaryFlag == true || hybridFormulaFlag == true){

						//Computes all caches and sets

						taxonName.setTitleCache(fullNameCache, true);

						taxonName.setFullTitleCache(taxonName.getFullTitleCache(), true);

						if (taxonName.isNonViral()){

							INonViralName nvn = taxonName;

							nvn.setNameCache(nameCache, true);

							nvn.setAuthorshipCache(nvn.getAuthorshipCache(), true);

						}

					}

					namesToSave.add(taxonName);

				}

				catch (UnknownCdmTypeException e) {

					logger.warn("Name with id " + nameId + " has unknown rankId " + " and could not be saved.");

					success = false;

				}

			} //while rs.hasNext()

		} catch (SQLException e) {

			logger.error("SQLException:" +  e);

			return false;

		}

//		logger.info( i + " names handled");

		getNameService().save(namesToSave);

		return success;

	}

	private Rank handleProlesAndRaceSublusus(BerlinModelImportState state, ResultSet rs, Rank rank) throws SQLException {

		Rank result;

		String rankAbbrev = rs.getString("RankAbbrev");

//		String rankStr = rs.getString("Rank");

		if (CdmUtils.nullSafeEqual(rankAbbrev, "prol.") ){

			result = Rank.PROLES();

		}else if(CdmUtils.nullSafeEqual(rankAbbrev, "race")){

			result = Rank.RACE();

		}else if(CdmUtils.nullSafeEqual(rankAbbrev, "sublusus")){

			result = Rank.SUBLUSUS();

		}else{

			result = rank;

			logger.warn("Unhandled rank: " + rankAbbrev);

		}

		return result;

	}

	@Override

	public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs, BerlinModelImportState state) {

		String nameSpace;

		Class<?> cdmClass;

		Set<String> idSet;

		Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();

		try{

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

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

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

			while (rs.next()){

				handleForeignKey(rs, teamIdSet, "AuthorTeamFk");

				handleForeignKey(rs, teamIdSet, "ExAuthorTeamFk");

				handleForeignKey(rs, teamIdSet, "BasAuthorTeamFk");

				handleForeignKey(rs, teamIdSet, "ExBasAuthorTeamFk");

				handleForeignKey(rs, referenceIdSet, "nomRefFk");

				handleForeignKey(rs, refDetailIdSet, "nomRefDetailFk");

			}

			//team map

			nameSpace = BerlinModelAuthorTeamImport.NAMESPACE;

			cdmClass = Team.class;

			idSet = teamIdSet;

			Map<String, Person> teamMap = (Map<String, Person>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, teamMap);

			//reference map

			nameSpace = BerlinModelReferenceImport.REFERENCE_NAMESPACE;

			cdmClass = Reference.class;

			idSet = referenceIdSet;

			Map<String, Reference> referenceMap = (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, referenceMap);

			//refDetail map

			nameSpace = BerlinModelRefDetailImport.REFDETAIL_NAMESPACE;

			cdmClass = Reference.class;

			idSet = refDetailIdSet;

			Map<String, Reference> refDetailMap= (Map<String, Reference>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

			result.put(nameSpace, refDetailMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	private boolean makeZoologialName(ResultSet rs, IZoologicalName zooName, int nameId)

					throws SQLException{

		boolean success = true;

		//publicationYear

		String authorTeamYear = rs.getString("authorTeamYear");

		try {

			if (! "".equals(CdmUtils.Nz(authorTeamYear).trim())){

				Integer publicationYear  = Integer.valueOf(authorTeamYear.trim());

				zooName.setPublicationYear(publicationYear);

			}

		} catch (NumberFormatException e) {

			logger.warn("authorTeamYear could not be parsed for taxonName: "+ nameId);

		}

		//original publication year

		String basAuthorTeamYear = rs.getString("basAuthorTeamYear");

		try {

			if (! "".equals(CdmUtils.Nz(basAuthorTeamYear).trim())){

				Integer OriginalPublicationYear  = Integer.valueOf(basAuthorTeamYear.trim());

				zooName.setOriginalPublicationYear(OriginalPublicationYear);

			}

		} catch (NumberFormatException e) {

			logger.warn("basAuthorTeamYear could not be parsed for taxonName: "+ nameId);

		}

		return success;

	}

	private boolean makeBotanicalNamePart(ResultSet rs, IBotanicalName botanicalName)throws SQLException{

		boolean success = true;

		String dbAttrName;

		String cdmAttrName;

		dbAttrName = "HybridFormulaFlag";

		cdmAttrName = "isHybridFormula";

		success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);

		dbAttrName = "MonomHybFlag";

		cdmAttrName = "isMonomHybrid";

		success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);

		dbAttrName = "BinomHybFlag";

		cdmAttrName = "isBinomHybrid";

		success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);

		dbAttrName = "TrinomHybFlag";

		cdmAttrName = "isTrinomHybrid";

		success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);

		try {

			String strCultivarGroupName = rs.getString("CultivarGroupName");

			String strCultivarName = rs.getString("CultivarName");

			if (botanicalName.isCultivar()){

				ICultivarPlantName cultivarName = (ICultivarPlantName)botanicalName;

				String concatCultivarName = CdmUtils.concat("-", strCultivarName, strCultivarGroupName);

				if (isNotBlank(strCultivarGroupName) && isNotBlank(strCultivarName)){

					logger.warn("CDM does not support cultivarGroupName and CultivarName together: " + concatCultivarName);

				}

				cultivarName.setCultivarName(strCultivarGroupName);

			}

		} catch (SQLException e) {

			throw e;

		}

		return success;

	}

	private boolean makeNomenclaturalReference(IImportConfigurator config, TaxonName taxonNameBase,

					int nameId, ResultSet rs, ResultSetPartitioner partitioner) throws SQLException{

		Map<String, Reference> refMap = partitioner.getObjectMap(BerlinModelReferenceImport.REFERENCE_NAMESPACE);

		Map<String, Reference> refDetailMap = partitioner.getObjectMap(BerlinModelRefDetailImport.REFDETAIL_NAMESPACE);

		Object nomRefFkObj = rs.getObject("NomRefFk");

		Object nomRefDetailFkObj = rs.getObject("NomRefDetailFk");

		boolean refDetailPrelim = rs.getBoolean("RefDetailPrelim");

		boolean success = true;

		//nomenclatural Reference

		if (refMap != null){

			if (nomRefFkObj != null){

				String nomRefFk = String.valueOf(nomRefFkObj);

				String nomRefDetailFk = String.valueOf(nomRefDetailFkObj);

				//get nomRef

				Reference nomReference =

					getReferenceFromMaps(refDetailMap, refMap, nomRefDetailFk, nomRefFk);

				//setNomRef

				if (nomReference == null ){

					//TODO

					if (! config.isIgnoreNull()){

						logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFk + ") for TaxonName (nameId = " + nameId + ")"+

							" was not found in reference store. Nomenclatural reference was not set!!");

					}

				}else{

					if (! INomenclaturalReference.class.isAssignableFrom(nomReference.getClass())){

						logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFk + ") for TaxonName (nameId = " + nameId + ")"+

								" is not assignable from INomenclaturalReference. (Class = " + nomReference.getClass()+ ")");

					}

					nomReference.setNomenclaturallyRelevant(true);

					taxonNameBase.setNomenclaturalReference(nomReference);

				}

			}

		}

		return success;

	}

	private static TeamOrPersonBase getAuthorTeam(Map<String, Team> teamMap, Object teamIdObject, int nameId, BerlinModelImportConfigurator bmiConfig){

		if (teamIdObject == null){

			return null;

		}else {

			String teamId = String.valueOf(teamIdObject);

			TeamOrPersonBase author = teamMap.get(teamId);

			if (author == null){

				//TODO

				if (!bmiConfig.isIgnoreNull() && ! (teamId.equals(0) && bmiConfig.isIgnore0AuthorTeam()) ){

					logger.warn("AuthorTeam (teamId = " + teamId + ") for TaxonName (nameId = " + nameId + ")"+

				" was not found in authorTeam store. Relation was not set!!");}

				return null;

			}else{

				return author;

			}

		}

	}

	@Override

	protected boolean doCheck(BerlinModelImportState state){

		IOValidator<BerlinModelImportState> validator = new BerlinModelTaxonNameImportValidator();

		return validator.validate(state);

	}

	@Override

    protected boolean isIgnore(BerlinModelImportState state){

		return ! state.getConfig().isDoTaxonNames();

	}

//FOR FUTURE USE , DONT DELETE

//	new CdmStringMapper("nameId", "nameId"),

//	new CdmStringMapper("rankFk", "rankFk"),

//	new CdmStringMapper("nameCache", "nameCache"),

//	new CdmStringMapper("unnamedNamePhrase", "unnamedNamePhrase"),

//	new CdmStringMapper("fullNameCache", "fullNameCache"),

//	new CdmStringMapper("preliminaryFlag", "preliminaryFlag"),

//	new CdmStringMapper("supragenericName", "supragenericName"),

//	new CdmStringMapper("genus", "genus"),

//	new CdmStringMapper("genusSubdivisionEpi", "genusSubdivisionEpi"),

//	new CdmStringMapper("speciesEpi", "speciesEpi"),

//	new CdmStringMapper("infraSpeciesEpi", "infraSpeciesEpi"),

//	new CdmStringMapper("authorTeamFk", "authorTeamFk"),

//	new CdmStringMapper("exAuthorTeamFk", "exAuthorTeamFk"),

//	new CdmStringMapper("basAuthorTeamFk", "basAuthorTeamFk"),

//	new CdmStringMapper("exBasAuthorTeamFk", "exBasAuthorTeamFk"),

//	new CdmStringMapper("hybridFormulaFlag", "hybridFormulaFlag"),

//	new CdmStringMapper("monomHybFlag", "monomHybFlag"),

//	new CdmStringMapper("binomHybFlag", "binomHybFlag"),

//	new CdmStringMapper("trinomHybFlag", "trinomHybFlag"),

//	new CdmStringMapper("cultivarGroupName", "cultivarGroupName"),

//	new CdmStringMapper("cultivarName", "cultivarName"),

//	new CdmStringMapper("nomRefFk", "nomRefFk"),

//	new CdmStringMapper("nomRefDetailFk", "nomRefDetailFk"),

//	new CdmStringMapper("nameSourceRefFk", "nameSourceRefFk"),

//	new CdmStringMapper("source_Acc", "source_Acc"),

//	new CdmStringMapper("created_When", "created_When"),

//	new CdmStringMapper("created_Who", "created_Who"),

//	new CdmStringMapper("notes", "notes"),

//	new CdmStringMapper("parsingComments", "parsingComments"),

//	new CdmStringMapper("oldNomRefFk", "oldNomRefFk"),

//	new CdmStringMapper("oldNomRefDetailFk", "oldNomRefDetailFk"),

//	new CdmStringMapper("updated_Who", "updated_Who"),

//	new CdmStringMapper("orthoProjection", "orthoProjection"),

}