EDIT

// $Id$

/**

* 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.sql.SQLException;

import java.util.ArrayList;

import java.util.HashMap;

import java.util.List;

import java.util.Set;

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.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.NameRelationship;

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

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

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

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.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

 * @date 23.02.2010

 *

 */

@Component

public class PesiRelTaxonExport extends PesiExportBase {

	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 HashMap<Rank, Rank> rank2endRankMap = new HashMap<Rank, Rank>();

	private List<Rank> rankList = new ArrayList<Rank>();

	private PesiExportMapping mapping;

	private int count = 0;

	private static NomenclaturalCode nomenclaturalCode2;

	public PesiRelTaxonExport() {

		super();

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.DbExportBase#getStandardMethodParameter()

	 */

	@Override

	public Class<? extends CdmBase> getStandardMethodParameter() {

		return standardMethodParameter;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)

	 */

	@Override

	protected boolean doCheck(PesiExportState state) {

		boolean result = true;

		return result;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)

	 */

	@Override

	protected void doInvoke(PesiExportState state) {

		try {

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

			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);

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

			mapping = getMapping();

			// Initialize the db mapper

			mapping.initialize(state);

			TransactionStatus txStatus = null;

			List<Classification> classificationList = null;

			// Specify starting ranks for tree traversing

			rankList.add(Rank.KINGDOM());

			rankList.add(Rank.GENUS());

			// Specify where to stop traversing (value) when starting at a specific Rank (key)

			rank2endRankMap.put(Rank.GENUS(), null); // Since NULL does not match an existing Rank, traverse all the way down to the leaves

			rank2endRankMap.put(Rank.KINGDOM(), Rank.GENUS()); // excludes rank genus

			// Retrieve list of classifications

			txStatus = startTransaction(true);

			logger.info("Started transaction. Fetching all classifications...");

			classificationList = getClassificationService().listClassifications(null, 0, null, null);

			commitTransaction(txStatus);

			logger.debug("Committed transaction.");

			logger.info("Fetched " + classificationList.size() + " classification(s).");

			for (Classification classification : classificationList) {

				for (Rank rank : rankList) {

					txStatus = startTransaction(true);

					logger.info("Started transaction to fetch all rootNodes specific to Rank " + rank.getLabel() + " ...");

					List<TaxonNode> rankSpecificRootNodes = getClassificationService().loadRankSpecificRootNodes(classification, rank, null);

					logger.info("Fetched " + rankSpecificRootNodes.size() + " RootNodes for Rank " + rank.getLabel());

					commitTransaction(txStatus);

					logger.debug("Committed transaction.");

					for (TaxonNode rootNode : rankSpecificRootNodes) {

						txStatus = startTransaction(false);

						Rank endRank = rank2endRankMap.get(rank);

						if (endRank != null) {

							logger.info("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till Rank " + endRank.getLabel() + " ...");

						} else {

							logger.info("Started transaction to traverse childNodes of rootNode (" + rootNode.getUuid() + ") till leaves are reached ...");

						}

						TaxonNode newNode = getTaxonNodeService().load(rootNode.getUuid());

						if (isPesiTaxon(newNode.getTaxon())){

							TaxonNode parentNode = newNode.getParent();

							success &=traverseTree(newNode, parentNode, endRank, state);

							commitTransaction(txStatus);

							logger.debug("Committed transaction.");

						}else{

							logger.debug("Taxon is not in PESI");

						}

					}

				}

			}

			logger.warn("*** Finished Making " + pluralString + " ..." + getSuccessString(success));

			if (!success){

				state.setUnsuccessfull();

			}

			return;

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.setUnsuccessfull();

			return;

		}

	}

	/**

	 * Traverses the classification recursively and stores determined values for every Taxon.

	 * @param childNode

	 * @param parentNode

	 * @param treeIndex

	 * @param fetchLevel

	 * @param state

	 */

	private boolean  traverseTree(TaxonNode childNode, TaxonNode parentNode, Rank fetchLevel, PesiExportState state) {

		boolean success = true;

		// Traverse all branches from this childNode until specified fetchLevel is reached.

		TaxonBase<?> childTaxon = childNode.getTaxon();

		if (childTaxon != null) {

			if (isPesiTaxon(childTaxon)){

				if (childTaxon.getName() != null) {

					Rank childTaxonNameRank = childTaxon.getName().getRank();

					if (childTaxonNameRank != null) {

						if (! childTaxonNameRank.equals(fetchLevel)) {

							success &= saveData(childNode, parentNode, state);

							for (TaxonNode newNode : childNode.getChildNodes()) {

								success &= traverseTree(newNode, childNode, fetchLevel, state);

							}

						} else {

	//						logger.error("Target Rank " + fetchLevel.getLabel() + " reached");

							return success;

						}

					} else {

						logger.warn("Rank is NULL. FetchLevel can not be checked: " + childTaxon.getUuid() + " (" + childTaxon.getTitleCache() + ")");

					}

				} else {

					logger.error("TaxonName is NULL for taxon: " + childTaxon.getUuid());

				}

			}else{

				logger.debug("Taxon is not a PESI taxon: " + childTaxon.getUuid());

			}

		} else {

			logger.error("Taxon is NULL for TaxonNode: " + childNode.getUuid());

		}

		return success;

	}

	/**

	 * Stores values in database for every recursive round.

	 * @param childNode

	 * @param parentNode

	 * @param treeIndex

	 * @param state

	 * @param currentTaxonFk

	 */

	private boolean saveData(TaxonNode childNode, TaxonNode parentNode, PesiExportState state) {

		boolean success = true;

		Taxon childNodeTaxon = childNode.getTaxon();

		if (childNodeTaxon != null) {

			// TaxonRelationships

			success &= saveTaxonRelationships(state, childNodeTaxon);

			// TaxonNameRelationships

			success &= saveNameRelationships(state, childNodeTaxon);

			// SynonymRelationships

			success &= saveSynonymAndSynNameRelationships(state, childNodeTaxon);

		}

		return success;

	}

	private boolean saveSynonymAndSynNameRelationships(PesiExportState state, Taxon childNodeTaxon) {

		boolean success = true;

		for (SynonymRelationship synRel : childNodeTaxon.getSynonymRelations()) { // synonyms of accepted taxon

			Synonym synonym = synRel.getSynonym();

			TaxonNameBase<?,?> synonymTaxonName = synonym.getName();

			if (! isPesiTaxon(synonym)){

				logger.warn("Synonym " + synonym.getId() + " of synonym relation " + synRel.getId() + " is not a PESI taxon. Can't export relationship");

				continue;

			}

			// Store synonym data in Taxon table

			invokeSynonyms(state, synonymTaxonName);

			Set<SynonymRelationship> synonymRelations = synonym.getSynonymRelations();

			state.setCurrentFromObject(synonym);

			for (SynonymRelationship synonymRelationship : synonymRelations) {  //needed? Maybe to make sure that there are no partial synonym relations missed ??

				try {

					if (neededValuesNotNull(synonymRelationship, state)) {

						doCount(count++, modCount, pluralString);

						success &= mapping.invoke(synonymRelationship);

					}

				} catch (SQLException e) {

					logger.error("SynonymRelationship (" + synonymRelationship.getUuid() + ") could not be stored : " + e.getMessage());

				}

			}

			// SynonymNameRelationship

			success &= saveNameRelationships(state, synonym);

		}

		return success;

	}

	private boolean saveNameRelationships(PesiExportState state, TaxonBase taxonBase) {

		boolean success = true;

		TaxonNameBase<?,?> childNodeTaxonName = taxonBase.getName();

		//from relations

		Set<NameRelationship> nameRelations = childNodeTaxonName.getRelationsFromThisName();

		state.setCurrentFromObject(taxonBase);

		boolean isFrom = true;

		success &= saveOneSideNameRelation(state, isFrom, nameRelations);

		//toRelations

		nameRelations = childNodeTaxonName.getRelationsToThisName();

		state.setCurrentToObject(taxonBase);

		isFrom = false;

		success &= saveOneSideNameRelation(state, isFrom, nameRelations);

		return success;

	}

	private boolean saveOneSideNameRelation(PesiExportState state, boolean isFrom, Set<NameRelationship> nameRelations) {

		boolean success = true;

		for (NameRelationship nameRelation : nameRelations) {

			try {

				TaxonNameBase<?,?> relatedName = isFrom ? nameRelation.getToName(): nameRelation.getFromName();

				if ( isPurePesiName(relatedName)){

					success &= checkAndInvokeNameRelation(state, nameRelation, relatedName, isFrom);

				}else{

					for (TaxonBase<?> relatedTaxon : getPesiTaxa(relatedName)){

						success &= checkAndInvokeNameRelation(state, nameRelation, relatedTaxon, isFrom);

					}

				}

			} catch (SQLException e) {

				logger.error("NameRelationship " + nameRelation.getUuid() + " for " + nameRelation.getFromName().getTitleCache() + " and " + nameRelation.getToName().getTitleCache() + " could not be created: " + e.getMessage());

				success = false;

			}

		}

		return success;

	}

	private boolean checkAndInvokeNameRelation(PesiExportState state, NameRelationship nameRelation, IdentifiableEntity<?> relatedObject, boolean isFrom) throws SQLException {

		boolean success = true;

		if (isFrom){

			state.setCurrentToObject(relatedObject);

		}else{

			state.setCurrentFromObject(relatedObject);

		}

		if (neededValuesNotNull(nameRelation, state)) {

			doCount(count++, modCount, pluralString);

			success &= mapping.invoke(nameRelation);

		}

		return success;

	}

	private boolean saveTaxonRelationships(PesiExportState state, Taxon childNodeTaxon) {

		boolean success = true;

		Taxon taxon = childNodeTaxon;

		Set<TaxonRelationship> taxonRelations = taxon.getRelationsToThisTaxon();

		for (TaxonRelationship taxonRelationship : taxonRelations) {

			try {

				if (neededValuesNotNull(taxonRelationship, state)) {

					doCount(count++, modCount, pluralString);

					success &= mapping.invoke(taxonRelationship);

				}

			} catch (SQLException e) {

				logger.error("TaxonRelationship could not be created for this TaxonRelation (" + taxonRelationship.getUuid() + "): " + e.getMessage());

			}

		}

		return success;

	}

	/**

	 * Determines synonym related data and saves them.

	 * @param state

	 * @param sr

	 */

	private static void invokeSynonyms(PesiExportState state, TaxonNameBase synonymTaxonName) {

		// Store KingdomFk and Rank information in Taxon table

		Integer kingdomFk = PesiTransformer.nomenClaturalCode2Kingdom(synonymTaxonName.getNomenclaturalCode());

		Integer synonymFk = state.getDbId(synonymTaxonName);

		saveSynonymData(synonymTaxonName, synonymTaxonName.getNomenclaturalCode(), kingdomFk, synonymFk);

	}

	/**

	 * Stores synonym data.

	 * @param taxonName

	 * @param nomenclaturalCode

	 * @param kingdomFk

	 * @param synonymParentTaxonFk

	 * @param currentTaxonFk

	 */

	private static boolean saveSynonymData(TaxonNameBase taxonName,

			NomenclaturalCode nomenclaturalCode, Integer kingdomFk,

			Integer currentSynonymFk) {

		try {

			if (kingdomFk != null) {

				synonymsStmt.setInt(1, kingdomFk);

			} else {

				synonymsStmt.setObject(1, null);

			}

			Integer rankFk = getRankFk(taxonName, nomenclaturalCode);

			if (rankFk != null) {

				synonymsStmt.setInt(2, rankFk);

			} else {

				synonymsStmt.setObject(2, null);

			}

			synonymsStmt.setString(3, getRankCache(taxonName, nomenclaturalCode));

			if (currentSynonymFk != null) {

				synonymsStmt.setInt(4, currentSynonymFk);

			} else {

				synonymsStmt.setObject(4, null);

			}

			synonymsStmt.executeUpdate();

			return true;

		} catch (SQLException e) {

			logger.error("SQLException during invoke for taxonName - " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + "): " + e.getMessage());

			e.printStackTrace();

			return false;

		}

	}

	/**

	 * Checks whether needed values for an entity are NULL.

	 * @return

	 */

	private boolean neededValuesNotNull(RelationshipBase<?, ?, ?> relationship, PesiExportState state) {

		boolean result = true;

		if (getTaxonFk1(relationship, state) == null) {

			logger.warn("TaxonFk1 is NULL, but is not allowed to be. Therefore no record was written to export database for this relationship: " + relationship.getUuid());

			result = false;

		}

		if (getTaxonFk2(relationship, state) == null) {

			logger.warn("TaxonFk2 is NULL, but is not allowed to be. Therefore no record was written to export database for this relationship: " + relationship.getUuid());

			result = false;

		}

		return result;

	}

	/**

	 * 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 = (PesiExportConfigurator) state.getConfig();

		String sql;

		Source destination =  pesiConfig.getDestination();

		// Clear RelTaxon

		sql = "DELETE FROM " + dbTableName;

		destination.setQuery(sql);

		destination.update(sql);

		return true;

	}

	/* (non-Javadoc)

	 * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IoStateBase)

	 */

	@Override

	protected boolean isIgnore(PesiExportState state) {

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

	}

	/**

	 * 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

	 */

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

		return getObjectFk(relationship, state, true);

	}

	/**

	 * 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

	 */

	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);

	}

	/**

	 * 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) {

		String result = null;

		NomenclaturalCode code = null;

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

			code = CdmBase.deproxy(relationship, TaxonRelationship.class).getToTaxon().getName().getNomenclaturalCode();

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

			code = CdmBase.deproxy(relationship, SynonymRelationship.class).getAcceptedTaxon().getName().getNomenclaturalCode();

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

			code = CdmBase.deproxy(relationship,  NameRelationship.class).getFromName().getNomenclaturalCode();

		}

		if (code != null) {

			result = PesiTransformer.taxonRelation2RelTaxonQualifierCache(relationship, code);

		} else {

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

		}

		return result;

	}

	/**

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

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

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getNotes(RelationshipBase<?, ?, ?> relationship) {

		// TODO

		return null;

	}

	/**

	 * 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(SynonymRelationship.class)) {

			SynonymRelationship sr = (SynonymRelationship)relationship;

			taxonBase = (isFrom) ? sr.getSynonym() : sr.getAcceptedTaxon();

		} else if (relationship.isInstanceOf(NameRelationship.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;

	}

	/**

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

	 * @param taxonName The {@link TaxonNameBase TaxonName}.

	 * @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.

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

	 * @see MethodMapper

	 */

	private static Integer getRankFk(TaxonNameBase taxonName, NomenclaturalCode nomenclaturalCode) {

		Integer result = null;

		if (nomenclaturalCode != null) {

			if (taxonName != null && taxonName.getRank() == null) {

				logger.warn("Rank is null: " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");

			}

			result = PesiTransformer.rank2RankId(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));

			if (result == null) {

				logger.warn("Rank could not be determined for PESI-Kingdom-Id " + PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode) + " and TaxonName " + taxonName.getUuid() + " (" + taxonName.getTitleCache() + ")");

			}

		}

		return result;

	}

	/**

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

	 * @param taxonName The {@link TaxonNameBase TaxonName}.

	 * @param nomenclaturalCode The {@link NomenclaturalCode NomenclaturalCode}.

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

	 * @see MethodMapper

	 */

	private static String getRankCache(TaxonNameBase taxonName, NomenclaturalCode nomenclaturalCode) {

		String result = null;

		if (nomenclaturalCode != null) {

			result = PesiTransformer.rank2RankCache(taxonName.getRank(), PesiTransformer.nomenClaturalCode2Kingdom(nomenclaturalCode));

		}

		return result;

	}

	/**

	 * Returns the CDM to PESI specific export mappings.

	 * @return The {@link PesiExportMapping PesiExportMapping}.

	 */

	private 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));

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

		return mapping;

	}

}