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.mexico;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.logging.log4j.LogManager;

import org.apache.logging.log4j.Logger;

import org.springframework.stereotype.Component;

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

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

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

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

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

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;

/**

 * @author a.mueller

 * @since 08.02.2022

 */

@Component

public class MexicoEfloraTaxonRelationImport extends MexicoEfloraImportBase {

    private static final long serialVersionUID = 8616047381536678637L;

    private static final Logger logger = LogManager.getLogger();

	protected static final String NAMESPACE = "TaxonRelation";

	private static final String pluralString = "Taxon relations";

	private static final String dbTableName = "EFlora_Taxonomia4CDM2";

	public MexicoEfloraTaxonRelationImport(){

		super(dbTableName, pluralString);

	}

	@Override

	protected String getIdQuery(MexicoEfloraImportState state) {

		String sql = " SELECT IdCAT "

		        + " FROM " + dbTableName + " t "

		        + " LEFT JOIN cv1_Controlled_vocabulary_for_name_Ranks r ON t.CategoriaTaxonomica = r.NombreCategoriaTaxonomica "

		        + " WHERE t.IdCAT_AscendenteHerarquico4CDM NOT IN ('2PLANT') "

		        + " ORDER BY r.Nivel1, IdCAT ";

		return sql;

	}

	@Override

	protected String getRecordQuery(MexicoEfloraImportConfigurator config) {

		String sqlSelect = " SELECT t.*, acc.uuid accUuid, p.uuid pUuid, bas.uuid basUuid, p.IDCat pID ";

		String sqlFrom = " FROM " + dbTableName + " t "

		        + " LEFT JOIN "+dbTableName+" acc ON acc.IdCat = t.IdCATRel "

		        + " LEFT JOIN "+dbTableName+" p ON p.IdCat = t.IdCAT_AscendenteHerarquico4CDM "

		        + " LEFT JOIN "+dbTableName+" bas ON bas.IdCat = t.IdCAT_BasNomOrig "

		        ;

		String sqlWhere = " WHERE ( t.IdCAT IN (" + ID_LIST_TOKEN + ") )";

		String strRecordQuery =sqlSelect + " " + sqlFrom + " " + sqlWhere ;

		return strRecordQuery;

	}

	@Override

	public boolean doPartition(@SuppressWarnings("rawtypes") ResultSetPartitioner partitioner, MexicoEfloraImportState state) {

	    classification = null;

	    boolean success = true ;

	    @SuppressWarnings("rawtypes")

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

		@SuppressWarnings("unchecked")

        Map<String, TaxonBase<?>> taxonMap = partitioner.getObjectMap(MexicoEfloraTaxonImport.NAMESPACE);

		ResultSet rs = partitioner.getResultSet();

		try{

			while (rs.next()){

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

				//create TaxonName element

			    String taxonId = rs.getString("IdCAT");

                UUID uuid = UUID.fromString(rs.getString("uuid"));

			    String accUuidStr = rs.getString("accUuid"); //accepted for synonym

			    String parentUuidStr = rs.getString("pUuid");  //parent

				String basUuidStr = rs.getString("basUuid"); //basionyms of accepted taxa

				String parentId = rs.getString("pID");

				if ("2PLANT".equals(parentId) || "79217TRACH".equals(parentId)) {

				    parentUuidStr = null;

				}

				TaxonBase<?> taxonBase = taxonMap.get(uuid.toString());

				try {

				    if (taxonBase == null) {

				        logger.warn(taxonId + ": Taxon does not exist");

				        continue;

				    }else if (taxonBase.isInstanceOf(Synonym.class) && accUuidStr != null) {

				        Synonym syn = CdmBase.deproxy(taxonBase, Synonym.class);

				        TaxonBase<?> related = taxonMap.get(accUuidStr);

				        if (!related.isInstanceOf(Taxon.class)){

				            logger.warn(taxonId + ":  Accepted taxon for synonym is not accepted: " + accUuidStr);

				        }else {

				            Taxon acc = CdmBase.deproxy(related, Taxon.class);

				            acc.addSynonym(syn, SynonymType.SYNONYM_OF);

				        }

				    }else if (taxonBase.isInstanceOf(Taxon.class) && parentUuidStr != null) {

                        Taxon child = CdmBase.deproxy(taxonBase, Taxon.class);

                        TaxonBase<?> parentBase = taxonMap.get(parentUuidStr);

                        if (!parentBase.isInstanceOf(Taxon.class)){

                            logger.warn(taxonId + ":  Parent is not accepted: " + parentUuidStr);

                        }else {

                            Taxon parent = CdmBase.deproxy(parentBase, Taxon.class);

                            Reference parentChildReference = null;

                            getClassification(state).addParentChild(parent, child, parentChildReference, null);

                        }

                    }else {

                        logger.warn(taxonId + ": Taxon has no valid relationship: " + taxonBase.getName().getTitleCache());

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

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

                            getClassification(state).addChildTaxon(taxon, null);

                        }

                    }

				    if (basUuidStr != null) {

				        TaxonName name = taxonBase.getName();

				        TaxonBase<?> basionymTaxon = taxonMap.get(basUuidStr);

				        name.addBasionym(basionymTaxon.getName());

				    }

					partitioner.startDoSave();

					taxaToSave.add(taxonBase);

				} catch (Exception e) {

					logger.warn("An exception (" +e.getMessage()+") occurred when trying to create relation for id " + taxonId + ". Relation could not be saved.");

					e.printStackTrace();

					success = false;

				}

			}

		} catch (Exception e) {

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

			return false;

		}

		getTaxonService().save(taxaToSave);

		logger.warn("Partition finished");

		return success;

	}

	Classification classification;

    private Classification getClassification(MexicoEfloraImportState state) {

        if (classification == null) {

            classification = getClassificationService().find(state.getConfig().getClassificationUuid());

            if (classification == null) {

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

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

                classification.setTitleCache(state.getConfig().getClassificationName(), true);

                getClassificationService().save(classification);

            }

        }

        return classification;

    }

    @Override

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

        String nameSpace;

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

		try{

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

			while (rs.next()){

                handleForeignUuidKey(rs, taxonIdSet, "uuid");

                handleForeignUuidKey(rs, taxonIdSet, "accUuid");

                handleForeignUuidKey(rs, taxonIdSet, "pUuid");

                handleForeignUuidKey(rs, taxonIdSet, "basUuid");

			}

            //taxon map

            nameSpace = MexicoEfloraTaxonImport.NAMESPACE;

            @SuppressWarnings("rawtypes")

            Map<String, TaxonBase> taxonMap = new HashMap<>();

            @SuppressWarnings("rawtypes")

            List<TaxonBase> taxa = getTaxonService().find(taxonIdSet);

            taxa.stream().forEach(t->taxonMap.put(t.getUuid().toString(), t));

            result.put(nameSpace, taxonMap);

		} catch (SQLException e) {

			throw new RuntimeException(e);

		}

		return result;

	}

	@Override

	protected String getTableName() {

		return dbTableName;

	}

	@Override

	public String getPluralString() {

		return pluralString;

	}

    @Override

    protected boolean doCheck(MexicoEfloraImportState state){

        return true;

    }

	@Override

	protected boolean isIgnore(MexicoEfloraImportState state){

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

	}

}