EDIT

/**

* Copyright (C) 2009 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.pesi.out;

import java.sql.Connection;

import java.sql.PreparedStatement;

import java.util.ArrayList;

import java.util.List;

import org.apache.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

import eu.etaxonomy.cdm.io.common.mapping.out.DbAnnotationMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedIntegerMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbFixedStringMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.DbObjectMapper;

import eu.etaxonomy.cdm.io.common.mapping.out.MethodMapper;

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

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

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

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

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

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

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

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

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.TaxonNode;

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

/**

 * The export class for relations between {@link eu.etaxonomy.cdm.model.taxon.TaxonBase TaxonBases}.<p>

 * Inserts into DataWarehouse database table <code>RelTaxon</code>.

 * @author e.-m.lee

 * @since 23.02.2010

 */

@Component

public class PesiRelTaxonExport extends PesiExportBase {

    private static final long serialVersionUID = 67808745337549629L;

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

    private static final Class<? extends CdmBase> standardMethodParameter = RelationshipBase.class;

	private static int modCount = 1000;

	private static final String dbTableName = "RelTaxon";

	private static final String pluralString = "Relationships";

	private static PreparedStatement synonymsStmt;

	private PesiExportMapping mapping;

	private PesiExportMapping synonymMapping;

	private PesiExportMapping taxonNodeMapping;

	private PesiExportMapping originalSpellingMapping;

	public PesiRelTaxonExport() {

		super();

	}

	@Override

	public Class<? extends CdmBase> getStandardMethodParameter() {

		return standardMethodParameter;

	}

	@Override

	protected void doInvoke(PesiExportState state) {

		try {

			logger.info("*** Started Making " + pluralString + " ...");

			doDelete(state);

			Connection connection = state.getConfig().getDestination().getConnection();

			String synonymsSql = "UPDATE Taxon SET KingdomFk = ?, RankFk = ?, RankCache = ? WHERE TaxonId = ?";

			synonymsStmt = connection.prepareStatement(synonymsSql);

			// Stores whether this invoke was successful or not.

			boolean success = true;

			// PESI: Clear the database table RelTaxon.

			//doDelete(state); -> done by stored procedure

			// Get specific mappings: (CDM) Relationship -> (PESI) RelTaxon

			mapping = getMapping();

			mapping.initialize(state);

			// Get specific mappings: (CDM) Synonym -> (PESI) RelTaxon

            synonymMapping = getSynonymMapping();

            synonymMapping.initialize(state);

            // Get specific mappings: (CDM) Synonym -> (PESI) RelTaxon

            taxonNodeMapping = getTaxonNodeMapping();

            taxonNodeMapping.initialize(state);

			//Export taxon relations

			success &= doPhase01(state, mapping);

			//Export taxon nodes

            success &= doPhase01b(state, taxonNodeMapping);

			// Export name relations

			success &= doPhase02(state, mapping);

	         // Export synonym relations (directly attached to taxa)

            success &= doPhase03(state, synonymMapping);

			if (! success){

				state.getResult().addError("An unknown error occurred in PesiRelTaxonExport");

			}

		} catch (Exception e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.getResult().addException(e);

			return;

		}

	}

    private boolean doPhase03(PesiExportState state, PesiExportMapping synonymMapping) {

        logger.info("PHASE 3: Direct Synonym Relationships ...");

        boolean success = true;

        int limit = state.getConfig().getLimitSave();

        // Start transaction

        TransactionStatus txStatus = startTransaction(true);

        logger.debug("Started new transaction. Fetching some synonyms (max: " + limit + ") ...");

        List<Synonym> list;

        //taxon relations

        int partitionCount = 0;

        int totalCount = 0;

        while ((list = getNextTaxonPartition(Synonym.class, limit, partitionCount++, null))!= null) {

            totalCount = totalCount + list.size();

            logger.info("Read " + list.size() + " PESI synonyms. Limit: " + limit + ". Total: " + totalCount );

//          if (list.size() > 0){

//              logger.warn("First relation type is " + list.get(0).getType().getTitleCache());

//          }

            for (Synonym synonym : list){

                try {

                    synonymMapping.invoke(synonym);

                } catch (Exception e) {

                    logger.error(e.getMessage() + ". Synonym: " +  synonym.getUuid());

                    e.printStackTrace();

                }

            }

            commitTransaction(txStatus);

            txStatus = startTransaction();

        }

        commitTransaction(txStatus);

        return success;

    }

    private boolean doPhase01(PesiExportState state, PesiExportMapping mapping) {

		logger.info("PHASE 1: Taxon Relationships ...");

		boolean success = true;

		int limit = state.getConfig().getLimitSave();

		// Start transaction

		TransactionStatus txStatus = startTransaction(true);

		logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");

		List<RelationshipBase<?,?,?>> list;

		//taxon relations

		int partitionCount = 0;

		int totalCount = 0;

		while ((list = getNextTaxonRelationshipPartition(limit, partitionCount++, null)) != null) {

			totalCount = totalCount + list.size();

			logger.info("Read " + list.size() + " PESI relations. Limit: " + limit + ". Total: " + totalCount );

//			if (list.size() > 0){

//				logger.warn("First relation type is " + list.get(0).getType().getTitleCache());

//			}

			for (RelationshipBase<?,?,?> rel : list){

				try {

					mapping.invoke(rel);

				} catch (Exception e) {

					logger.error(e.getMessage() + ". Relationship: " +  rel.getUuid());

					e.printStackTrace();

				}

			}

			commitTransaction(txStatus);

			txStatus = startTransaction();

		}

		commitTransaction(txStatus);

		return success;

	}

    private boolean doPhase01b(PesiExportState state, PesiExportMapping taxonNodeMapping) {

        logger.info("PHASE 1b: Taxonnodes ...");

        boolean success = true;

        int limit = state.getConfig().getLimitSave();

        // Start transaction

        TransactionStatus txStatus = startTransaction(true);

        logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");

        List<TaxonNode> list;

        //taxon nodes

        int partitionCount = 0;

        int totalCount = 0;

        while ((list = getNextTaxonNodePartition(limit, partitionCount++, null)) != null) {

            totalCount = totalCount + list.size();

            logger.info("Read " + list.size() + " PESI taxon nodes. Limit: " + limit + ". Total: " + totalCount );

            for (TaxonNode tn : list){

                try {

                    taxonNodeMapping.invoke(tn);

                } catch (Exception e) {

                    logger.error(e.getMessage() + ". TaxonNode: " +  tn.getUuid());

                    e.printStackTrace();

                }

            }

            commitTransaction(txStatus);

            txStatus = startTransaction();

        }

        commitTransaction(txStatus);

        return success;

    }

	private boolean doPhase02(PesiExportState state, PesiExportMapping mapping2) {

		logger.info("PHASE 2: Name Relationships ...");

		boolean success = true;

		int limit = state.getConfig().getLimitSave();

		// Start transaction

		TransactionStatus txStatus = startTransaction(true);

		logger.debug("Started new transaction. Fetching some " + pluralString + " (max: " + limit + ") ...");

		//name relations

		List<NameRelationship> list;

		int partitionCount = 0;

		while ((list = getNextNameRelationshipPartition(NameRelationship.class, limit, partitionCount++, null)) != null   ) {

			txStatus = handleNameRelationList(state, txStatus, list);

		}

        //hybrid relations

		List<HybridRelationship> hybridList;

		partitionCount = 0;

        while ((hybridList = getNextNameRelationshipPartition(HybridRelationship.class, limit, partitionCount++, null)) != null   ) {

            txStatus = handleNameRelationList(state, txStatus, hybridList);

        }

        //original spellings

        List<NomenclaturalSource> originalSpellingList;

        partitionCount = 0;

        while ((originalSpellingList = getNextOriginalSpellingPartition(limit, partitionCount++, null)) != null   ) {

            txStatus = handleOriginalSpellingList(state, txStatus, originalSpellingList);

        }

        commitTransaction(txStatus);

		logger.info("End PHASE 2: Name Relationships ...");

		state.setCurrentFromObject(null);

		state.setCurrentToObject(null);

		return success;

	}

    private TransactionStatus handleNameRelationList(PesiExportState state, TransactionStatus txStatus,

            List<? extends RelationshipBase<?,?,?>> list) {

        for (RelationshipBase<?,?,?> rel : list){

        	try {

        	    TaxonName name1;

        	    TaxonName name2;

        		if (rel.isInstanceOf(HybridRelationship.class)){

        			HybridRelationship hybridRel = CdmBase.deproxy(rel, HybridRelationship.class);

        			name1 = hybridRel.getParentName();

        			name2 = hybridRel.getHybridName();

        		}else if (rel.isInstanceOf(NameRelationship.class)){

        			NameRelationship nameRel = CdmBase.deproxy(rel, NameRelationship.class);

        			name1 = nameRel.getFromName();

        			name2 = nameRel.getToName();

        		}else{

        			logger.warn ("Only hybrid- and name-relationships allowed here");

        			continue;

        		}

        		List<IdentifiableEntity> fromList = new ArrayList<>();

        		List<IdentifiableEntity> toList = new ArrayList<>();

        		makeList(name1, fromList);

        		makeList(name2, toList);

        		for (IdentifiableEntity<?> fromEntity : fromList){

        			for (IdentifiableEntity<?> toEntity : toList){

        				//TODO set entities to state

        				state.setCurrentFromObject(fromEntity);

        				state.setCurrentToObject(toEntity);

        				mapping.invoke(rel);

        			}

        		}

        	} catch (Exception e) {

        		logger.error(e.getMessage() + ". Relationship: " +  rel.getUuid());

        		e.printStackTrace();

        	}

        }

        commitTransaction(txStatus);

        txStatus = startTransaction();

        return txStatus;

    }

    private TransactionStatus handleOriginalSpellingList(PesiExportState state, TransactionStatus txStatus,

            List<NomenclaturalSource> list) {

        for (NomenclaturalSource nomSource : list){

            try {

                TaxonName name1 = nomSource.getNameUsedInSource();

                TaxonName name2 = nomSource.getSourcedName();

                List<IdentifiableEntity> fromList = new ArrayList<>();

                List<IdentifiableEntity> toList = new ArrayList<>();

                makeList(name1, fromList);

                makeList(name2, toList);

                for (IdentifiableEntity<?> fromEntity : fromList){

                    for (IdentifiableEntity<?> toEntity : toList){

                        //TODO set entities to state

                        state.setCurrentFromObject(fromEntity);

                        state.setCurrentToObject(toEntity);

                        originalSpellingMapping.invoke(nomSource);

                    }

                }

            } catch (Exception e) {

                logger.error(e.getMessage() + ". NomenclaturalSource: " +  nomSource.getUuid());

                e.printStackTrace();

            }

        }

        commitTransaction(txStatus);

        txStatus = startTransaction();

        return txStatus;

    }

	private void makeList(TaxonName name, List<IdentifiableEntity> list) {

		if (! hasPesiTaxon(name)){

			list.add(name);

		}else{

			for (TaxonBase<?> taxon: getPesiTaxa(name)){

				list.add(taxon);

			}

		}

	}

	/**

	 * Deletes all entries of database tables related to <code>RelTaxon</code>.

	 * @param state The {@link PesiExportState PesiExportState}.

	 * @return Whether the delete operation was successful or not.

	 */

	protected boolean doDelete(PesiExportState state) {

		PesiExportConfigurator pesiConfig = state.getConfig();

		Source destination =  pesiConfig.getDestination();

		// Clear RelTaxon

		String sql = "DELETE FROM " + dbTableName;

		destination.update(sql);

		return true;

	}

	/**

	 * Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.

	 * @param relationship The {@link RelationshipBase Relationship}.

	 * @param state The {@link PesiExportState PesiExportState}.

	 * @return The <code>TaxonFk1</code> attribute.

	 * @see MethodMapper

	 */

    @SuppressWarnings("unused")

	private static Integer getTaxonFk1(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {

		return getObjectFk(relationship, state, true);

	}

	/**

     * Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>TaxonRelationship</code>.

     * @param relationship The {@link RelationshipBase Relationship}.

     * @param state The {@link PesiExportState PesiExportState}.

     * @return The <code>TaxonFk1</code> attribute.

     * @see MethodMapper

     */

    @SuppressWarnings("unused")

    private static Integer getTaxonFk1(Synonym synonym, PesiExportState state) {

        return synonym.getAcceptedTaxon().getId();

    }

    /**

     * Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>Synonym</code>.

     * @param synonym The {@link Synonym synonym}.

     * @param state The {@link PesiExportState PesiExportState}.

     * @return The <code>TaxonFk1</code> attribute.

     * @see MethodMapper

     */

    @SuppressWarnings("unused")

    private static Integer getSynonym(Synonym synonym, PesiExportState state) {

        return state.getDbId(synonym);

    }

    /**

     * Returns the <code>TaxonFk1</code> attribute. It corresponds to a CDM <code>Synonym</code>.

     * @param synonym The {@link Synonym synonym}.

     * @param state The {@link PesiExportState PesiExportState}.

     * @return The <code>TaxonFk1</code> attribute.

     * @see MethodMapper

     */

    @SuppressWarnings("unused")

    private static Integer getParent(TaxonNode taxonNode, PesiExportState state) {

        TaxonNode parent = taxonNode == null? null : taxonNode.getParent();

        Taxon parentTaxon = parent == null? null: parent.getTaxon();

        return state.getDbId(parentTaxon);

    }

    /**

     * Returns the id of the previously defined fromObject.

     * @see MethodMapper

     */

    @SuppressWarnings("unused")

    private static Integer getFromObject(PesiExportState state) {

        return state.getDbId(state.getCurrentFromObject());

    }

    /**

     * Returns the id of the previously defined fromObject.

     * @see MethodMapper

     */

    @SuppressWarnings("unused")

    private static Integer getToObject(PesiExportState state) {

        return state.getDbId(state.getCurrentToObject());

    }

	/**

	 * Returns the <code>TaxonFk2</code> attribute. It corresponds to a CDM <code>SynonymRelationship</code>.

	 * @param relationship The {@link RelationshipBase Relationship}.

	 * @param state The {@link PesiExportState PesiExportState}.

	 * @return The <code>TaxonFk2</code> attribute.

	 * @see MethodMapper

	 */

    @SuppressWarnings("unused")

	private static Integer getTaxonFk2(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {

		return getObjectFk(relationship, state, false);

	}

	/**

	 * Returns the <code>RelTaxonQualifierFk</code> attribute.

	 * @param relationship The {@link RelationshipBase Relationship}.

	 * @return The <code>RelTaxonQualifierFk</code> attribute.

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static Integer getRelTaxonQualifierFk(RelationshipBase<?, ?, ?> relationship) {

		return PesiTransformer.taxonRelation2RelTaxonQualifierFk(relationship);

	}

    @SuppressWarnings("unused")

    private static Integer getRelTaxonQualifierFk(Synonym synonym) {

        return PesiTransformer.synonym2RelTaxonQualifierFk(synonym);

    }

	/**

	 * Returns the <code>RelQualifierCache</code> attribute.

	 * @param relationship The {@link RelationshipBase Relationship}.

	 * @return The <code>RelQualifierCache</code> attribute.

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getRelQualifierCache(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {

		String result = null;

		NomenclaturalCode code = null;

		Taxon taxon = null;

		TaxonName name= null;

		if (relationship.isInstanceOf(TaxonRelationship.class)){

			TaxonRelationship rel = CdmBase.deproxy(relationship, TaxonRelationship.class);

			taxon = rel.getToTaxon();

			name = taxon.getName();

			code = name.getNameType();

		}else if (relationship.isInstanceOf(NameRelationship.class)){

			NameRelationship rel = CdmBase.deproxy(relationship,  NameRelationship.class);

			name = rel.getFromName();

			code =name.getNameType();

		}else if (relationship.isInstanceOf(HybridRelationship.class)){

			HybridRelationship rel =  CdmBase.deproxy(relationship,  HybridRelationship.class);

			name = rel.getParentName();

			code = name.getNameType();

		}

		if (code != null) {

			result = state.getConfig().getTransformer().getCacheByRelationshipType(relationship, code);

		} else {

			logger.error("NomenclaturalCode is NULL while creating the following relationship: " + relationship.getUuid());

		}

		return result;

	}

	/**

	 * Returns the database key of an object in the given relationship.

	 * @param relationship {@link RelationshipBase RelationshipBase}.

	 * @param state {@link PesiExportState PesiExportState}.

	 * @param isFrom A boolean value indicating whether the database key of the parent or child in this relationship is searched. <code>true</code> means the child is searched. <code>false</code> means the parent is searched.

	 * @return The database key of an object in the given relationship.

	 */

	private static Integer getObjectFk(RelationshipBase<?, ?, ?> relationship, PesiExportState state, boolean isFrom) {

		TaxonBase<?> taxonBase = null;

		if (relationship.isInstanceOf(TaxonRelationship.class)) {

			TaxonRelationship tr = (TaxonRelationship)relationship;

			taxonBase = (isFrom) ? tr.getFromTaxon():  tr.getToTaxon();

		} else if (relationship.isInstanceOf(NameRelationship.class)

		        || relationship.isInstanceOf(HybridRelationship.class)) {

			if (isFrom){

				return state.getDbId(state.getCurrentFromObject());

			}else{

				return state.getDbId(state.getCurrentToObject());

			}

		}

		if (taxonBase != null) {

			if (! isPesiTaxon(taxonBase)){

				logger.warn("Related taxonBase is not a PESI taxon. Taxon: " + taxonBase.getId() + "/" + taxonBase.getUuid() + "; TaxonRel: " +  relationship.getId() + "(" + relationship.getType().getTitleCache() + ")");

				return null;

			}else{

				return state.getDbId(taxonBase);

			}

		}

		logger.warn("No taxon found in state for relationship: " + relationship.toString());

		return null;

	}

   private static Integer getObjectFk(NomenclaturalSource nomSource, PesiExportState state, boolean isFrom) {

        if (isFrom){

            return state.getDbId(state.getCurrentFromObject());

        }else{

            return state.getDbId(state.getCurrentToObject());

        }

    }

    @SuppressWarnings("unused")  //for synonym mapping

    private static String getSynonymTypeCache(Synonym synonym, PesiExportState state) {

        String result = null;

        NomenclaturalCode code = null;

        code = synonym.getAcceptedTaxon().getName().getNameType();

        if (code != null) {

            result = state.getConfig().getTransformer().getCacheBySynonymType(synonym, code);

        } else {

            logger.error("NomenclaturalCode is NULL while creating the following synonym: " + synonym.getUuid());

        }

        return result;

    }

	/**

	 * Returns the CDM to PESI specific export mappings.

	 * @return The {@link PesiExportMapping PesiExportMapping}.

	 */

	PesiExportMapping getMapping() {

		PesiExportMapping mapping = new PesiExportMapping(dbTableName);

		mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getTaxonFk1", standardMethodParameter, PesiExportState.class));

		mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getTaxonFk2", standardMethodParameter, PesiExportState.class));

		mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this));

		mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this, RelationshipBase.class, PesiExportState.class));

		mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));

		return mapping;

	}

	/**

     * Returns the CDM to PESI specific export mappings.

     * @return The {@link PesiExportMapping PesiExportMapping}.

     */

    PesiExportMapping getSynonymMapping() {

        PesiExportMapping mapping = new PesiExportMapping(dbTableName);

        mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getSynonym", Synonym.class, PesiExportState.class));

        mapping.addMapper(DbObjectMapper.NewInstance("acceptedTaxon", "TaxonFk2"));

        mapping.addMapper(MethodMapper.NewInstance("RelTaxonQualifierFk", this, Synonym.class));

        mapping.addMapper(MethodMapper.NewInstance("RelQualifierCache", this.getClass(), "getSynonymTypeCache", Synonym.class, PesiExportState.class));

        mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));

        return mapping;

    }

    PesiExportMapping getTaxonNodeMapping() {

        PesiExportMapping mapping = new PesiExportMapping(dbTableName);

        mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getParent", TaxonNode.class, PesiExportState.class));

        mapping.addMapper(DbObjectMapper.NewInstance("taxon", "TaxonFk1"));

        mapping.addMapper(DbFixedIntegerMapper.NewInstance(PesiTransformer.IS_TAXONOMICALLY_INCLUDED_IN, "RelTaxonQualifierFk"));

        mapping.addMapper(DbFixedStringMapper.NewInstance("is taxonomically included in", "RelQualifierCache"));

//        mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));

        return mapping;

    }

    PesiExportMapping getOriginalSpellingMapping() {

        PesiExportMapping mapping = new PesiExportMapping(dbTableName);

        mapping.addMapper(MethodMapper.NewInstance("TaxonFk1", this.getClass(), "getFromObject", PesiExportState.class));

        mapping.addMapper(MethodMapper.NewInstance("TaxonFk2", this.getClass(), "getToObject", PesiExportState.class));

        mapping.addMapper(DbFixedIntegerMapper.NewInstance(PesiTransformer.IS_ORIGINAL_SPELLING_FOR, "RelTaxonQualifierFk"));

        mapping.addMapper(DbFixedStringMapper.NewInstance("is original spelling for", "RelQualifierCache"));

//        mapping.addMapper(DbAnnotationMapper.NewExludedInstance(getLastActionAnnotationTypes(), "Notes"));

        return mapping;

    }

    @Override

    protected boolean doCheck(PesiExportState state) {

        return true;

    }

    @Override

    protected boolean isIgnore(PesiExportState state) {

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

    }

}