EDIT

/**

* Copyright (C) 2015 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.edaphobase;

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.io.common.IPartitionedIO;

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

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

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

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

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

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

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

/**

 * Import class for synonym relationships in Edaphobase.

 *

 * @author a.mueller

 * @since 21.12.2015

 *

 */

@Component

public class EdaphobaseSynonymyImport extends EdaphobaseImportBase {

    private static final long serialVersionUID = 6641343927320994726L;

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

    private static final String tableName = "tax_synonym";

    private static final String pluralString = "related synonyms";

    /**

     * @param tableName

     * @param pluralString

     */

    public EdaphobaseSynonymyImport() {

        super(tableName, pluralString);

    }

    @Override

    protected String getIdQuery(EdaphobaseImportState state) {

        return "    SELECT sr.tax_synonym_id  "

                + " FROM tax_synonym sr "

                + "  INNER JOIN tax_taxon s ON s.taxon_id = sr.a_taxon_fk_taxon_id "

                + "  INNER JOIN tax_taxon t ON t.taxon_id = sr.b_taxon_fk_taxon_id "

                + " WHERE  s.valid = false AND t.valid = true AND sr.synonym_role = 11614 "

                + " ORDER BY sr.a_taxon_fk_taxon_id ";

    }

    @Override

    protected String getRecordQuery(EdaphobaseImportConfigurator config) {

        String result = "SELECT sr.* "

                + " FROM tax_synonym sr"

                + " WHERE tax_synonym_id IN (@IDSET)";

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

        return result;

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, EdaphobaseImportState state) {

        ResultSet rs = partitioner.getResultSet();

        Reference sourceReference = state.getTransactionalSourceReference();

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

        try {

            while (rs.next()){

                int id = rs.getInt("tax_synonym_id");

                 //parentTaxonFk

//                boolean isValid = rs.getBoolean("valid");

                Integer synId = nullSafeInt(rs, "a_taxon_fk_taxon_id");

                Integer accId = nullSafeInt(rs, "b_taxon_fk_taxon_id");

                if (synId == null || accId == null){

                    logger.warn("Either a_taxon or b_taxon is NULL for tax_synonym " + id);

                }else{

                    TaxonBase<?> synonymCandidate = state.getRelatedObject(TAXON_NAMESPACE, String.valueOf(synId), TaxonBase.class);

                    if (synonymCandidate == null){

                        logger.warn("Synonym " + synId + " not found for synonymRelations (tax_synonym): " + id);

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

                        String message = "Synonym ("+synId+") is not synonym but accepted (valid). Can't add synonym for tax_synonym: "+id;

                        logger.warn(message);

                    }else{

                        Synonym synonym = CdmBase.deproxy(synonymCandidate, Synonym.class);

                        TaxonBase<?> accepted = state.getRelatedObject(TAXON_NAMESPACE, String.valueOf(accId), TaxonBase.class);

                        if (accepted == null){

                            logger.warn("Accepted(parent) taxon " + accId + " not found for tax_synonym " + id );

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

                            String message = "Taxon ("+accId+") is not accepted but synonym. Can't add synonym for tax_synonym: "+id;

                            logger.warn(message);

                        }else{

                            Taxon taxon = CdmBase.deproxy(accepted, Taxon.class);

                            if (synonym.getAcceptedTaxon()!= null){

                                String message = "Synonym ("+synId+") already has an accepted taxon. Have to clone synonym. RelId: " + id;

                                logger.warn(message);

                                synonym = (Synonym)synonym.clone();

                            }

                            taxon.addSynonym(synonym, SynonymType.SYNONYM_OF());

                            state.addSynonymWithAcceptedTaxon(synId);

                            taxaToSave.add(synonym);

                            taxaToSave.add(taxon);

                        }

                    }

                }

//              //id

//              String nameSpace = "tax_taxon";

//              ImportHelper.setOriginalSource(taxonBase, state.getTransactionalSourceReference(), id, nameSpace);

//              ImportHelper.setOriginalSource(name, state.getTransactionalSourceReference(), id, nameSpace);

            }

        } catch (SQLException e) {

            e.printStackTrace();

        }

        getTaxonService().saveOrUpdate(taxaToSave);

        return true;

    }

    @Override

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

            EdaphobaseImportState state) {

        String nameSpace;

        Class<?> cdmClass;

        Set<String> idSet;

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

        try{

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

            while (rs.next()){

                handleForeignKey(rs, taxonIdSet, "a_taxon_fk_taxon_id");

                handleForeignKey(rs, taxonIdSet, "b_taxon_fk_taxon_id");

            }

            //name map

            nameSpace = TAXON_NAMESPACE;

            cdmClass = TaxonBase.class;

            idSet = taxonIdSet;

            @SuppressWarnings("rawtypes")

            Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);

            result.put(nameSpace, taxonMap);

        } catch (SQLException e) {

            throw new RuntimeException(e);

        }

        return result;

    }

    @Override

    protected boolean doCheck(EdaphobaseImportState state) {

        return true;

    }

    @Override

    protected boolean isIgnore(EdaphobaseImportState state) {

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

    }

}