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

/**

 * Import class for synonym relationships in edaphobase.

 *

 * @author a.mueller

 * @date 21.12.2015

 *

 */

@Component

public class EdaphobaseSynonymy2Import extends EdaphobaseImportBase {

    private static final long serialVersionUID = 8968205268798472136L;

    private static final Logger logger = Logger.getLogger(EdaphobaseSynonymy2Import.class);

    private static final String tableName = "tax_synonym";

    private static final String pluralString = "related unreal synonyms";

    /**

     * @param tableName

     * @param pluralString

     */

    public EdaphobaseSynonymy2Import() {

        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  NOT (s.valid = false AND t.valid = true) OR sr.synonym_role <> 11614 "

                + " ORDER BY sr.a_taxon_fk_taxon_id ";

    }

    @Override

    protected String getRecordQuery(EdaphobaseImportConfigurator config) {

        String result = "SELECT sr.* , t2.valid t2valid, t3.valid t3valid, t2.taxon_id t2taxon_id, t3.taxon_id t3taxon_id "

                + " FROM tax_taxon s "

                + "  INNER JOIN tax_synonym sr 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 "

                + "  LEFT JOIN tax_synonym sr2 ON t.taxon_id = sr2.a_taxon_fk_taxon_id "

                + "  LEFT JOIN tax_taxon t2 ON t2.taxon_id =    sr2.b_taxon_fk_taxon_id "

                + "  LEFT JOIN tax_synonym sr3 ON t2.taxon_id = sr3.a_taxon_fk_taxon_id"

                + "  LEFT JOIN tax_taxon t3 ON t3.taxon_id =    sr3.b_taxon_fk_taxon_id "

                + " WHERE sr.tax_synonym_id IN (@IDSET)"

                + " ORDER BY sr.tax_synonym_id ";

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

        return result;

    }

    @Override

    public boolean doPartition(ResultSetPartitioner partitioner, EdaphobaseImportState state) {

        ResultSet rs = partitioner.getResultSet();

        Map<String, TaxonBase> map = partitioner.getObjectMap(TAXON_NAMESPACE);

        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");

                Integer role = nullSafeInt(rs, "synonym_role");

                boolean isSynonym = role.equals(11614);

                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 (isSynonym && 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 if (!isSynonym && !synonymCandidate.isInstanceOf(Taxon.class)){

                        String message = "From taxon  ("+synId+") in included in relation is not of type Taxon but Synonym (invalid). Can't add concept relation for tax_synonym: "+id;

                        logger.warn(message);

                    }else if(isSynonym){

                        handleSynonymToInvalid(state, rs, taxaToSave, synId, accId, synonymCandidate);

                    }else{

                       handleConceptRelationship(state, taxaToSave, id, accId, role, synonymCandidate);

                    }

                }

//              //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;

    }

    /**

     * @param state

     * @param taxaToSave

     * @param id

     * @param accId

     * @param role

     * @param synonymCandidate

     */

    private void handleConceptRelationship(EdaphobaseImportState state, Set<TaxonBase> taxaToSave, int id,

                Integer accId, Integer role, TaxonBase<?> fromTaxonBase) {

           if (!role.equals(11613)){

               String message = "Concept relation is not of type is included in ('11613'). This is not expected here. tax_synonym: " + id;

               logger.warn(message);

           }else{

               Taxon fromTaxon = CdmBase.deproxy(fromTaxonBase, Taxon.class);

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

               if (toTaxonBase == null){

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

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

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

                   logger.warn(message);

               }else{

                   Taxon toTaxon = CdmBase.deproxy(toTaxonBase, Taxon.class);

                   TaxonRelationshipType relType = TaxonRelationshipType.INCLUDES();

                   toTaxon.addTaxonRelation(fromTaxon, relType, null, null);

                   taxaToSave.add(fromTaxon);

                   taxaToSave.add(toTaxon);

               }

           }

    }

    /**

     * @param state

     * @param taxaToSave

     * @param synId

     * @param accId

     * @param synonymCandidate

     * @throws SQLException

     */

    private void handleSynonymToInvalid(EdaphobaseImportState state, ResultSet rs, Set<TaxonBase> taxaToSave, Integer synId,

            Integer accId, TaxonBase<?> synonymCandidate) throws SQLException {

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

        if (state.hasAcceptedTaxon(synId)){

            //TODO do some further homotypie checking

        }else{

            String message = "Synonym a("+synId+") of invalid taxon (b) has not accepted taxon yet. Automatically create relationship to valid taxon (c) of invalid taxon (b) ";

            logger.warn(message);

            Integer acc3 = nullSafeInt(rs, "t3taxon_id");

            Boolean valid3 = nullSafeBoolean(rs, "t3valid");

            Integer acc2 = nullSafeInt(rs, "t2taxon_id");

            Boolean valid2 = nullSafeBoolean(rs, "t2valid");

            Integer accC  = acc2;

            if (valid2 == null || valid2 == false){

                accC = acc3;

                if (valid3 == null || valid3 == false){

                    logger.warn("All unvalid not handled: " + synId);

                }

            }

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

            if (acceptedC == null || acceptedC.isInstanceOf(Synonym.class)){

                logger.warn("Taxon c does not exist or is not valid taxon.");

            }else{

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

                //TODO

                SynonymType synType = SynonymType.SYNONYM_OF();

                taxon.addSynonym(synonym, synType);

                taxaToSave.add(synonym);

                taxaToSave.add(taxon);

            }

        }

    }

    @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<>();

            while (rs.next()){

                handleForeignKey(rs, taxonIdSet, "a_taxon_fk_taxon_id");

                handleForeignKey(rs, taxonIdSet, "b_taxon_fk_taxon_id");

                handleForeignKey(rs, taxonIdSet, "t2taxon_id");

                handleForeignKey(rs, taxonIdSet, "t3taxon_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();

    }

}