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.SQLException;

import java.util.ArrayList;

import java.util.EnumSet;

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.IExportConfigurator.DO_REFERENCES;

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.io.pesi.erms.ErmsTransformer;

import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;

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

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

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

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

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

/**

 * The export class for {@link eu.etaxonomy.cdm.model.reference.Reference References}.<p>

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

 *

 * @author e.-m.lee

 * @since 11.02.2010

 */

@Component

public class PesiSourceExport extends PesiExportBase {

    private static final long serialVersionUID = -3084883718722120651L;

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

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

	private static int modCount = 5000;

	public static final String dbTableName = "Source";

	private static final String pluralString = "Sources";

	List<Integer> storedSourceIds = new ArrayList<>();

	public PesiSourceExport() {

		super();

	}

	@Override

	public Class<? extends CdmBase> getStandardMethodParameter() {

		return standardMethodParameter;

	}

	/**

	 * Checks whether a sourceId was stored already.

	 * @param sourceId

	 * @return

	 */

	protected boolean isStoredSourceId(Integer sourceId) {

		if (storedSourceIds.contains(sourceId)) {

			return true;

		} else {

			return false;

		}

	}

	/**

	 * Adds a sourceId to the list of storedSourceIds.

	 * @param sourceId

	 */

	protected void addToStoredSourceIds(Integer sourceId) {

		if (! storedSourceIds.contains(sourceId)) {

			this.storedSourceIds.add(sourceId);

		}

	}

	@Override

	protected void doInvoke(PesiExportState state) {

		try{

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

			// Get the limit for objects to save within a single transaction.

			int limit = modCount;//pesiExportConfigurator.getLimitSave();

			// Stores whether this invoke was successful or not.

			boolean success = true ;

			// PESI: Clear the database table Source.

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

			// Get specific mappings: (CDM) Reference -> (PESI) Source

			PesiExportMapping mapping = getMapping();

			// Initialize the db mapper

			mapping.initialize(state);

			// Create the Sources

			int count = 0;

			int pastCount = 0;

			TransactionStatus txStatus = null;

			List<Reference> list = null;

//			logger.warn("PHASE 1...");

			// Start transaction

			txStatus = startTransaction(true);

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

			while ((list = getReferenceService().list(null, limit, count, null, null)).size() > 0) {

				logger.debug("Fetched " + list.size() + " " + pluralString + ". Exporting...");

				for (Reference reference : list) {

					doCount(count++, modCount, pluralString);

					success &= mapping.invoke(reference);

				}

				// Commit transaction

				commitTransaction(txStatus);

				logger.debug("Committed transaction.");

				logger.info("Exported " + (count - pastCount) + " " + pluralString + ". Total: " + count);

				pastCount = count;

				// Start transaction

				txStatus = startTransaction(true);

				if (logger.isDebugEnabled()) {

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

                }

			}

			if (list.size() == 0) {

				logger.info("No " + pluralString + " left to fetch.");

			}

			// Commit transaction

			commitTransaction(txStatus);

			logger.info("Committed transaction.");

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

			if (!success){

				state.getResult().addError("An error occurred in PesiSourceExport.invoke");

			}

			return;

		} catch (SQLException e) {

			e.printStackTrace();

			logger.error(e.getMessage());

			state.getResult().addException(e);

			return;

		}

	}

	/**

	 * Deletes all entries of database tables related to <code>Source</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 Sources

		String sql = "DELETE FROM " + dbTableName;

		destination.setQuery(sql);

		destination.update(sql);

		return true;

	}

	/**

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

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static Integer getIMIS_Id(Reference reference) {

		return null;

	}

	/**

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

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static Integer getSourceCategoryFK(Reference reference) {

		Integer result = null;

		try {

		    result = PesiTransformer.reference2SourceCategoryFK(reference);

		} catch (Exception e) {

			e.printStackTrace();

		}

		return result;

	}

	/**

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

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getSourceCategoryCache(Reference reference, PesiExportState state) {

		return state.getTransformer().getCacheByReference(reference);

	}

	/**

	 * Returns the <code>Name</code> attribute. The corresponding CDM attribute is <code>title</code>.

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getName(Reference reference) {

		if (reference != null) {

		    String titleCache = reference.getTitleCache();

		    //handling copied from DbObjectMapper

		    if (titleCache == null || titleCache.length()>250 || titleCache.endsWith("...")){

                Set<String> fullCache = reference.getExtensions(ExtensionType.uuidExtNonTruncatedCache);

                if (!fullCache.isEmpty()){

                    if (fullCache.size()>1){

                        logger.warn("Reference has more than 1 'Non truncated cache' extensions. This should not happen. Arbitrary one taken.");

                    }

                    String value = fullCache.iterator().next();

                    if(isNotBlank(value)){

                        titleCache = value;

                    }

                }

            }

		    return titleCache == null ? null : titleCache.trim();

		} else {

			return null;

		}

	}

	/**

	 * Returns the <code>AuthorString</code> attribute. The corresponding CDM attribute is the <code>titleCache</code> of an <code>authorTeam</code>.

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getAuthorString(Reference reference) {

		String result = null;

		Set<Extension> extensions;

		try {

    		if (reference != null) {

    			TeamOrPersonBase<?> team = reference.getAuthorship();

    			if (team != null) {

    				result = team.getTitleCache();

    			}else if (!reference.getExtensions(ErmsTransformer.uuidExtAuthor).isEmpty()){

    			    result = reference.getExtensions(ErmsTransformer.uuidExtAuthor).iterator().next();

    			}

    		}

		} catch (Exception e) {

			e.printStackTrace();

		}

		return result;

	}

	/**

	 * Returns the <code>NomRefCache</code> attribute. The corresponding CDM attribute is <code>titleCache</code>.

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getNomRefCache(Reference reference) {

		return null;

//		if (reference != null) {

//			return reference.getTitleCache();

//		} else {

//			return null;

//		}

	}

	/**

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

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getRefIdInSource(Reference reference) {

		String result = null;

		try {

    		if (reference != null) {

    			Set<IdentifiableSource> sourceAll = reference.getSources();

    			Set<IdentifiableSource> sourceCandidates = filterPesiSources(sourceAll);

    			if (sourceCandidates.size() == 1) {

    				result = sourceCandidates.iterator().next().getIdInSource();

    			} else if (sourceCandidates.size() > 1) {

    				logger.warn("Reference for RefIdInSource has multiple IdentifiableSources which are candidates for a PESI originalDbSource. RefIdInSource can't be determined correctly and will be left out: " + reference.getUuid() + " (" + reference.getTitleCache() + ")");

    				int count = 1;

    //				for (IdentifiableSource source : sources) {

    //					result += source.getIdInSource();

    //					if (count < sources.size()) {

    //						result += "; ";

    //					}

    //					count++;

    //				}

    			}

    		}

		} catch (Exception e) {

			e.printStackTrace();

		}

		return result;

	}

//	private static Set<IdentifiableSource> filterOriginalPesiDbSources(

//			Set<IdentifiableSource> sourceAll) {

//		Set<IdentifiableSource> sourceCandidates = new HashSet<>();

//		for (IdentifiableSource source : sourceAll){

//			if (isOriginalPesiDbSource(source)){

//				sourceCandidates.add(source);

//			}

//		}

//		return sourceCandidates;

//	}

//

//	private static boolean isOriginalPesiDbSource(IdentifiableSource source) {

//		return (source.getCitation() != null) &&

//				source.getCitation().getType().equals(ReferenceType.Database);

//	}

	/**

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

	 * @param reference The {@link Reference Reference}.

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

	 * @see MethodMapper

	 */

	@SuppressWarnings("unused")

	private static String getOriginalDB(Reference reference) {

	    //TODO may not work for E+M and FauEu as they may not have import sources for all data

	    EnumSet<PesiSource> sources  = getSources(reference);

	    return PesiTransformer.getOriginalDbBySources(sources);

//	    String result = "";

//

//		try {

//    		if (reference != null) {

//    			Set<IdentifiableSource> sourcesAll = reference.getSources();

//    			Set<IdentifiableSource> sourceCandidates = filterOriginalPesiDbSources(sourcesAll);

//

//    			if (sourceCandidates.size() == 1) {

//    				Reference citation = sourceCandidates.iterator().next().getCitation();

//    				if (citation != null) {

//    					result = PesiTransformer.databaseString2Abbreviation(citation.getTitleCache()); //or just title

//    				} else {

//    					logger.warn("OriginalDB can not be determined because the citation of this source is NULL: " + sourceCandidates.iterator().next().getUuid());

//    				}

//    			} else if (sourceCandidates.size() > 1) {

//    				logger.warn("Taxon has multiple IdentifiableSources: " + reference.getUuid() + " (" + reference.getTitleCache() + ")");

//    				int count = 1;

//    				for (IdentifiableSource source : sourceCandidates) {

//    					Reference citation = source.getCitation();

//    					if (citation != null) {

//    						result += PesiTransformer.databaseString2Abbreviation(citation.getTitleCache());

//    						if (count < sourceCandidates.size()) {

//    							result += "; ";

//    						}

//    						count++;

//    					}

//    				}

//    			} else {

//    				result = null;

//    			}

//    		}

//		} catch (Exception e) {

//			e.printStackTrace();

//		}

//

//		return result;

	}

    @Override

    protected boolean doCheck(PesiExportState state) {

        return true;

    }

	@Override

	protected boolean isIgnore(PesiExportState state) {

		return ! state.getConfig().getDoReferences().equals(DO_REFERENCES.ALL);

	}

	/**

	 * Returns the CDM to PESI specific export mappings.

	 * @return The {@link PesiExportMapping PesiExportMapping}.

	 */

	private PesiExportMapping getMapping() {

		PesiExportMapping mapping = new PesiExportMapping(dbTableName);

		mapping.addMapper(IdMapper.NewInstance("SourceId"));

		// IMIS_Id

		ExtensionType imisExtensionType = (ExtensionType)getTermService().find(ErmsTransformer.uuidExtImis);

		if (imisExtensionType != null) {

			mapping.addMapper(DbExtensionMapper.NewInstance(imisExtensionType, "IMIS_Id"));

		} else {

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

		}

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

		mapping.addMapper(MethodMapper.NewInstance("SourceCategoryCache", this, Reference.class, PesiExportState.class));

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

		mapping.addMapper(DbStringMapper.NewInstance("referenceAbstract", "Abstract"));

		mapping.addMapper(DbStringMapper.NewInstance("title", "Title"));

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

		mapping.addMapper(DbTimePeriodMapper.NewInstance("datePublished", "RefYear"));

		mapping.addMapper(DbDoiMapper.NewInstance("doi", "Doi"));

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

		logger.warn("URI mapping needs to be combined");

//		mapping.addMapper(DbUriMapper.NewInstance("uri", "Link"));

		mapping.addMapper(DbExtensionMapper.NewInstance(ExtensionType.URL(), "Link"));

		mapping.addMapper(DbAnnotationMapper.NewInstance((String)null, "Notes"));

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

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

		return mapping;

	}

}