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.ResultSetPartitioner;

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

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

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

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

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

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

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

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

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

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

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

/**

 *

 * @author pplitzner

 * @date Mar 1, 2016

 *

 */

@Component

@SuppressWarnings("serial")

public class RedListGefaesspflanzenImportClassification extends DbImportBase<RedListGefaesspflanzenImportState, RedListGefaesspflanzenImportConfigurator> {

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

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

    private static final String pluralString = "classifications";

    public RedListGefaesspflanzenImportClassification() {

        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) {

        makeClassification(state);

        super.doInvoke(state);

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, RedListGefaesspflanzenImportState state) {

        ResultSet rs = partitioner.getResultSet();

        Classification gesamtListeClassification = getClassificationService().load(state.getConfig().getClassificationUuid());

        Classification checklistClassification = getClassificationService().load(RedListUtil.checkListClassificationUuid);

        try {

            while (rs.next()){

                makeSingleTaxonNode(state, rs, gesamtListeClassification, checklistClassification);

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        logger.info("Update classification (1000 nodes)");

        getClassificationService().saveOrUpdate(gesamtListeClassification);

        getClassificationService().saveOrUpdate(checklistClassification);

        return true;

    }

    private void makeSingleTaxonNode(RedListGefaesspflanzenImportState state, ResultSet rs, Classification gesamtListeClassification, Classification checklistClassification)

            throws SQLException {

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

        String parentId = String.valueOf(rs.getLong(RedListUtil.LOWER));

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

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

        //Gesamtliste

        TaxonBase taxonBaseGL = state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);

        Taxon parentGL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, parentId, TaxonBase.class);

        createParentChildNodes(gesamtListeClassification, id, gueltString, taxZusatzString, taxonBaseGL, parentGL);

        //Checkliste

        TaxonBase taxonBaseCL = state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, String.valueOf(id), TaxonBase.class);

        Taxon parentCL = (Taxon) state.getRelatedObject(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, parentId, TaxonBase.class);

        if(taxonBaseCL!=null){//null check necessary because not all taxa exist in the checklist

            createParentChildNodes(checklistClassification, id, gueltString, taxZusatzString, taxonBaseCL, parentCL);

        }

        if(taxonBaseGL!= null && taxonBaseCL!=null

                && taxonBaseGL.getUuid().equals(taxonBaseCL.getUuid())){

            RedListUtil.logMessage(id, "Same UUID for "+taxonBaseGL+ " (Gesamtliste) and "+taxonBaseCL+" (Checkliste", logger);

        }

        if(parentGL!=null && parentCL!=null && parentGL.getUuid().equals(parentCL.getUuid())){

            RedListUtil.logMessage(id, "Same UUID for "+parentGL+ " (Gesamtliste) and "+parentCL+" (Checkliste", logger);

        }

    }

    private void createParentChildNodes(Classification classification, long id, String gueltString,

            String taxZusatzString, TaxonBase taxonBase, Taxon parent) {

        if(taxonBase==null){

            RedListUtil.logMessage(id, "child taxon/synonym of "+parent+"  is null. ("+classification.getTitleCache()+")" , logger);

            return;

        }

        //taxon

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

            //misapplied name

            String appendedPhrase = taxonBase.getAppendedPhrase();

            if(appendedPhrase!=null && appendedPhrase.equals(RedListUtil.AUCT)){

                if(parent==null){

                    RedListUtil.logMessage(id, "parent taxon of misapplied name "+taxonBase+"  is null. ("+classification.getTitleCache()+")" , logger);

                    return;

                }

                parent.addMisappliedName((Taxon) taxonBase, null, null);

            }

            else{

                classification.addParentChild(parent, (Taxon)taxonBase, null, null);

            }

            if(CdmUtils.isNotBlank(taxZusatzString)){

                if(taxZusatzString.trim().equals("p. p.")){

                    RedListUtil.logMessage(id, "pro parte for accepted taxon "+taxonBase, logger);

                }

            }

        }

        //synonym

        else if(taxonBase.isInstanceOf(Synonym.class)){

            if(parent==null){

                RedListUtil.logMessage(id, "parent taxon of synonym "+taxonBase+"  is null. ("+classification.getTitleCache()+")" , logger);

                return;

            }

            //basionym

            if(gueltString.equals(RedListUtil.GUELT_BASIONYM)){

                parent.addHomotypicSynonym((Synonym) taxonBase, null, null);

                parent.getName().addBasionym(taxonBase.getName());

            }

            //regular synonym

            else{

                SynonymRelationship synonymRelationship = parent.addSynonym((Synonym) taxonBase, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null);

                //TAX_ZUSATZ

                if(CdmUtils.isNotBlank(taxZusatzString)){

                    if(taxZusatzString.trim().equals("p. p.")){

                        synonymRelationship.setProParte(true);

                    }

                    else if(taxZusatzString.trim().equals("s. l. p. p.")){

                        synonymRelationship.setProParte(true);

                        taxonBase.setAppendedPhrase("s. l.");

                    }

                    else if(taxZusatzString.trim().equals("s. str. p. p.")){

                        synonymRelationship.setProParte(true);

                        taxonBase.setAppendedPhrase("s. str.");

                    }

                    else if(taxZusatzString.trim().equals("s. l.")

                            || taxZusatzString.trim().equals("s. str.")){

                        taxonBase.setAppendedPhrase(taxZusatzString);

                    }

                    else{

                        RedListUtil.logMessage(id, "unknown value "+taxZusatzString+" for column "+RedListUtil.TAX_ZUSATZ, logger);

                    }

                }

            }

        }

        //set sec reference

        taxonBase.setSec(classification.getReference());

        taxonBase.setTitleCache(null, false);//refresh title cache

    }

    @Override

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

            RedListGefaesspflanzenImportState state) {

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

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

        try {

            while (rs.next()){

                idSet.add(String.valueOf(rs.getLong(RedListUtil.NAMNR)));

                idSet.add(String.valueOf(rs.getLong(RedListUtil.LOWER)));

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        Map<String, TaxonBase> taxonMapGesamtListe = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_GESAMTLISTE_NAMESPACE);

        result.put(RedListUtil.TAXON_GESAMTLISTE_NAMESPACE, taxonMapGesamtListe);

        Map<String, TaxonBase> taxonMapCheckliste = (Map<String, TaxonBase>) getCommonService().getSourcedObjectsByIdInSource(TaxonBase.class, idSet, RedListUtil.TAXON_CHECKLISTE_NAMESPACE);

        result.put(RedListUtil.TAXON_CHECKLISTE_NAMESPACE, taxonMapCheckliste);

        return result;

    }

    private void makeClassification(RedListGefaesspflanzenImportState state) {

        //Gesamtliste

        Classification classification = Classification.NewInstance(state.getConfig().getClassificationName());

        classification.setName(LanguageString.NewInstance("Gesamtliste", Language.DEFAULT()));

        classification.setUuid(state.getConfig().getClassificationUuid());

        Reference gesamtListeReference = ReferenceFactory.newGeneric();

        gesamtListeReference.setUuid(RedListUtil.gesamtListeReferenceUuid);

        gesamtListeReference.setTitle("Gesamtliste");

        classification.setReference(gesamtListeReference);

        getClassificationService().save(classification);

        //checkliste

        Classification checklistClassification = Classification.NewInstance("Checkliste");

        checklistClassification.setUuid(RedListUtil.checkListClassificationUuid);

        Reference checklistReference = ReferenceFactory.newGeneric();

        checklistReference.setUuid(RedListUtil.checkListReferenceUuid);

        checklistReference.setTitle("Checkliste");

        checklistClassification.setReference(checklistReference);

        getClassificationService().save(checklistClassification);

    }

    @Override

    protected boolean doCheck(RedListGefaesspflanzenImportState state) {

        return false;

    }

    @Override

    protected boolean isIgnore(RedListGefaesspflanzenImportState state) {

        return false;

    }

}