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.redlist.gefaesspflanzen;

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 org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import eu.etaxonomy.cdm.common.CdmUtils;

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

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

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

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

import eu.etaxonomy.cdm.io.common.mapping.UndefinedTransformerMethodException;

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

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

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

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

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

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

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

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

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.model.taxon.TaxonRelationship;

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

/**

 *

 * @author pplitzner

 * @date Mar 1, 2016

 *

 */

@Component

@SuppressWarnings("serial")

public class RedListGefaesspflanzenImportNames extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {

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

    private static final String tableName = "Rote Liste Gefäßpflanzen";

    private static final String pluralString = "names";

    public RedListGefaesspflanzenImportNames() {

        super(tableName, pluralString);

    }

    @Override

    protected String getIdQuery(RedListGefaesspflanzenImportState state) {

        return "SELECT NAMNR "

                + "FROM V_TAXATLAS_D20_EXPORT t "

                + " ORDER BY NAMNR";

    }

    @Override

    protected String getRecordQuery(RedListGefaesspflanzenImportConfigurator config) {

        String result = " SELECT * "

                + " FROM V_TAXATLAS_D20_EXPORT t "

                + " WHERE t.NAMNR IN (@IDSET)";

        result = result.replace("@IDSET", IPartitionedIO.ID_LIST_TOKEN);

        return result;

    }

    @Override

    protected void doInvoke(RedListGefaesspflanzenImportState state) {

        super.doInvoke(state);

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {

        ResultSet rs = partitioner.getResultSet();

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

        Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();

        try {

            while (rs.next()){

                makeSingleNameAndTaxon(state, rs, namesToSave, taxaToSave);

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        getNameService().saveOrUpdate(namesToSave);

        getTaxonService().saveOrUpdate(taxaToSave);

        return true;

    }

    private void makeSingleNameAndTaxon(RedListGefaesspflanzenImportState state, ResultSet rs, Set<TaxonNameBase> namesToSave, Set<TaxonBase> taxaToSave)

            throws SQLException {

        long id = rs.getLong(RedListUtil.NAMNR);

        String taxNameString = rs.getString(RedListUtil.TAXNAME);

        String gueltString = rs.getString(RedListUtil.GUELT);

        String rangString = rs.getString(RedListUtil.RANG);

        String ep1String = rs.getString(RedListUtil.EPI1);

        String ep2String = rs.getString(RedListUtil.EPI2);

        String ep3String = rs.getString(RedListUtil.EPI3);

        String nomZusatzString = rs.getString(RedListUtil.NOM_ZUSATZ);

        String taxZusatzString = rs.getString(RedListUtil.TAX_ZUSATZ);

        String zusatzString = rs.getString(RedListUtil.ZUSATZ);

        String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);

        String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);

        String hybString = rs.getString(RedListUtil.HYB);

        //---NAME---

        if(CdmUtils.isBlank(taxNameString) && CdmUtils.isBlank(ep1String)){

            RedListUtil.logMessage(id, "No name found!", logger);

        }

        Rank rank = makeRank(id, state, rangString);

        BotanicalName name = BotanicalName.NewInstance(rank);

        //ep1 should always be present

        if(CdmUtils.isBlank(ep1String)){

            RedListUtil.logMessage(id, RedListUtil.EPI1+" is empty!", logger);

        }

        name.setGenusOrUninomial(ep1String);

        if(CdmUtils.isNotBlank(ep2String)){

            name.setSpecificEpithet(ep2String);

        }

        if(CdmUtils.isNotBlank(ep3String)){

            if(rank==Rank.SUBSPECIES() ||

                    rank==Rank.VARIETY()){

                name.setInfraSpecificEpithet(ep3String);

            }

        }

        //nomenclatural status

        if(CdmUtils.isNotBlank(nomZusatzString)){

            NomenclaturalStatusType status = makeNomenclaturalStatus(id, state, nomZusatzString);

            if(status!=null){

                name.addStatus(NomenclaturalStatus.NewInstance(status));

            }

        }

        //hybrid

        if(hybString.equals(RedListUtil.HYB_X)){

            name.setBinomHybrid(true);

        }

        else if(hybString.equals(RedListUtil.HYB_XF)){

            name.setTrinomHybrid(true);

        }

        //--- AUTHORS ---

        //combination author

        if(authorKombString.contains(RedListUtil.EX)){

            //TODO: what happens with multiple ex authors??

            String[] kombSplit = authorKombString.split(RedListUtil.EX);

            if(kombSplit.length!=2){

                RedListUtil.logMessage(id, "Multiple ex combination authors found", logger);

            }

            for (int i = 0; i < kombSplit.length; i++) {

                if(i==0){

                    //first author is ex author

                    TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);

                    name.setExCombinationAuthorship(authorKomb);

                }

                else{

                    TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, kombSplit[i]);

                    name.setCombinationAuthorship(authorKomb);

                }

            }

        }

        else if(authorKombString.trim().contains(RedListUtil.AUCT)){

            RedListUtil.logMessage(id, "AUCT information in "+RedListUtil.AUTOR_KOMB+" column", logger);

        }

        else if(CdmUtils.isNotBlank(authorKombString)){

            TeamOrPersonBase authorKomb = (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorKombString);

            name.setCombinationAuthorship(authorKomb);

        }

        //basionym author

        if(authorBasiString.contains(RedListUtil.EX)){

            String[] basiSplit = authorBasiString.split(RedListUtil.EX);

            for (int i = 0; i < basiSplit.length; i++) {

                if(basiSplit.length!=2){

                    RedListUtil.logMessage(id, "Multiple ex basionymn authors found", logger);

                }

                if(i==0){

                    TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);

                    if(CdmUtils.isBlank(authorKombString)){

                        name.setExCombinationAuthorship(authorBasi);

                    }

                    else{

                        name.setExBasionymAuthorship(authorBasi);

                    }

                }

                else{

                    TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, basiSplit[i]);

                    if(CdmUtils.isBlank(authorKombString)){

                        name.setCombinationAuthorship(authorBasi);

                    }

                    else{

                        name.setBasionymAuthorship(authorBasi);

                    }

                }

            }

        }

        else if(CdmUtils.isNotBlank(authorBasiString)){

            //this seems to be a convention in the source database: When there is only a single author then only the "AUTOR_BASI" column is used

            TeamOrPersonBase authorBasi= (TeamOrPersonBase) state.getRelatedObject(RedListUtil.AUTHOR_NAMESPACE, authorBasiString);

            if(CdmUtils.isBlank(authorKombString)){

                name.setCombinationAuthorship(authorBasi);

            }

            else{

                name.setBasionymAuthorship(authorBasi);

            }

        }

        //check authorship consistency

        String authorString = rs.getString(RedListUtil.AUTOR);

        String authorshipCache = name.getAuthorshipCache();

        if(CdmUtils.isNotBlank(zusatzString)){

            authorString = authorString.replace(", "+zusatzString, "");

        }

        if(CdmUtils.isNotBlank(nomZusatzString)){

            authorString = authorString.replace(", "+nomZusatzString, "");

        }

        if(CdmUtils.isNotBlank(taxZusatzString)){

            authorString = authorString.replace(", "+taxZusatzString, "");

        }

        if(authorString.equals(RedListUtil.AUCT)){

            authorString = "";

        }

        if(!authorString.equals(authorshipCache)){

            RedListUtil.logMessage(id, "Authorship inconsistent! name.authorhshipCache <-> Column "+RedListUtil.AUTOR+": "+authorshipCache+" <-> "+authorString, logger);

        }

        //id

        ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, RedListUtil.NAME_NAMESPACE);

        state.getNameMap().put(id, name.getUuid());

        namesToSave.add(name);

        //---TAXON---

        TaxonBase taxonBase = null;

        if(authorBasiString.trim().contains(RedListUtil.AUCT)){

            taxonBase = Taxon.NewInstance(name, null);

            taxonBase.setAppendedPhrase(RedListUtil.AUCT);

        }

        else if(gueltString.equals(RedListUtil.GUELT_ACCEPTED_TAXON)){

            taxonBase = Taxon.NewInstance(name, null);

        }

        else if(gueltString.equals(RedListUtil.GUELT_SYNONYM) || gueltString.equals(RedListUtil.GUELT_BASIONYM)){

            taxonBase = Synonym.NewInstance(name, null);

        }

        if(taxonBase==null){

            RedListUtil.logMessage(id, "Taxon for name "+name+" could not be created.", logger);

            return;

        }

        //check taxon name consistency

        if(taxNameString.endsWith("agg.")){

            taxNameString = taxNameString.replace("agg.", "aggr.");

        }

        if(hybString.equalsIgnoreCase(RedListUtil.HYB_X)){

            taxNameString = taxNameString.replace("× ", "×");//hybrid sign has no space after it in titleCache for binomial hybrids

        }

        String nameCache = ((BotanicalName)taxonBase.getName()).getNameCache().trim();

        if(!taxNameString.trim().equals(nameCache)){

            RedListUtil.logMessage(id, "Taxon name inconsistent! taxon.titleCache <-> Column "+RedListUtil.TAXNAME+": "+nameCache+" <-> "+taxNameString, logger);

        }

        /*check if taxon/synonym is also in checklist

         * 1. create new taxon with the same name (in the checklist classification)

         * 2. create congruent concept relationship between both

         */

        String clTaxonString = rs.getString(RedListUtil.CL_TAXON);

        if(CdmUtils.isNotBlank(clTaxonString) && !clTaxonString.trim().equals("-")){

            TaxonBase clone = (TaxonBase) taxonBase.clone();

            clone.setName(name);

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

                TaxonRelationship taxonRelation = ((Taxon) taxonBase).addTaxonRelation((Taxon) clone, TaxonRelationshipType.CONGRUENT_TO(), null, null);

                taxonRelation.setDoubtful(true);//TODO Ist das mit " mit Fragezeichen" gemeint?

            }

            ImportHelper.setOriginalSource(clone, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);

            taxaToSave.add(clone);

        }

        //NOTE: the source has to be added after cloning or otherwise the clone would also get the source

        ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);

        taxaToSave.add(taxonBase);

    }

    private Rank makeRank(long id, RedListGefaesspflanzenImportState state, String rankStr) {

        Rank rank = null;

        try {

            rank = state.getTransformer().getRankByKey(rankStr);

        } catch (UndefinedTransformerMethodException e) {

            e.printStackTrace();

        }

        if(rank==null){

            RedListUtil.logMessage(id, rankStr+" could not be associated to a known rank.", logger);

        }

        return rank;

    }

    private NomenclaturalStatusType makeNomenclaturalStatus(long id, RedListGefaesspflanzenImportState state, String nomZusatzString) {

        NomenclaturalStatusType status = null;

        try {

            status = state.getTransformer().getNomenclaturalStatusByKey(nomZusatzString);

        } catch (UndefinedTransformerMethodException e) {

            e.printStackTrace();

        }

        if(status==null){

            RedListUtil.logMessage(id, nomZusatzString+" could not be associated to a known nomenclatural status.", logger);

        }

        return status;

    }

    @Override

    public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs,

            RedListGefaesspflanzenImportState state) {

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

        Map<String, AgentBase<?>> authorMap = new HashMap<String, AgentBase<?>>();

        try {

            while (rs.next()){

                String authorKombString = rs.getString(RedListUtil.AUTOR_KOMB);

                if(authorKombString.contains(RedListUtil.EX)){

                    String[] kombSplit = authorKombString.split(RedListUtil.EX);

                    for (int i = 0; i < kombSplit.length; i++) {

                        if(!authorMap.containsKey(kombSplit[i])){

                            authorMap.put(kombSplit[i], getAgentService().load(state.getAuthorMap().get(kombSplit[i])));

                        }

                    }

                }

                else if(CdmUtils.isNotBlank(authorKombString) && !authorMap.containsKey(authorKombString)){

                    authorMap.put(authorKombString, getAgentService().load(state.getAuthorMap().get(authorKombString)));

                }

                String authorBasiString = rs.getString(RedListUtil.AUTOR_BASI);

                //basionym author

                if(authorBasiString.contains(RedListUtil.EX)){

                    String[] basiSplit = authorBasiString.split(RedListUtil.EX);

                    for (int i = 0; i < basiSplit.length; i++) {

                        if(!authorMap.containsKey(basiSplit[i])){

                            authorMap.put(basiSplit[i], getAgentService().load(state.getAuthorMap().get(basiSplit[i])));

                        }

                    }

                }

                else if(CdmUtils.isNotBlank(authorBasiString) && !authorMap.containsKey(authorBasiString)){

                    authorMap.put(authorBasiString, getAgentService().load(state.getAuthorMap().get(authorBasiString)));

                }

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        result.put(RedListUtil.AUTHOR_NAMESPACE, authorMap);

        return result;

    }

    @Override

    protected boolean doCheck(RedListGefaesspflanzenImportState state) {

        return false;

    }

    @Override

    protected boolean isIgnore(RedListGefaesspflanzenImportState state) {

        return false;

    }

}