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.pilotOutputHtml;

import java.io.File;

import java.io.FileOutputStream;

import java.io.OutputStreamWriter;

import java.io.PrintWriter;

import java.util.List;

import org.apache.logging.log4j.LogManager;import org.apache.logging.log4j.Logger;

import org.springframework.stereotype.Component;

import org.springframework.transaction.TransactionStatus;

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

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

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

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

import eu.etaxonomy.cdm.io.sdd.out.SDDDataSet;

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

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

import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;

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

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.term.DefinedTermBase;

import eu.etaxonomy.cdm.model.term.TermType;

/**

 * @author h.fradin (from a.babadshanjan)

 * @since 10.12.2008

 */

@Component("pilotOutputExporter")

public class PilotOutputExporter

        extends CdmExportBase<PilotOutputExportConfigurator, PilotOutputExportState, IExportTransformer, File>

        implements ICdmExport<PilotOutputExportConfigurator, PilotOutputExportState> {

// public class JaxbExport extends CdmIoBase implements ICdmIoExport {

// TODO: public class JaxbExport extends CdmIoBase implements ICdmIO {

    private static final long serialVersionUID = -5556376038773540067L;

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

	private PilotOutputDocumentBuilder pilotOutputDocumentBuilder = null;

	private boolean doOccurrence = true;

	public PilotOutputExporter() {

		super();

		this.ioName = this.getClass().getSimpleName();

	}

	/** Retrieves data from a CDM DB and serializes them CDM to XML.

	 * Starts with root taxa and traverses the classification to retrieve children taxa, synonyms and relationships.

	 * Taxa that are not part of the classification are not found.

	 *

	 * @param exImpConfig

	 * @param dbname

	 * @param filename

	 */

	@Override

	protected void doInvoke(PilotOutputExportState state){

//		protected boolean doInvoke(IExportConfigurator config,

//		Map<String, MapWrapper<? extends CdmBase>> stores) {

		PilotOutputExportConfigurator pilotOutputExpConfig = state.getConfig();

		String dbname = pilotOutputExpConfig.getSource().getName();

    	String fileName = pilotOutputExpConfig.getDestinationNameString();

		logger.info("Serializing DB " + dbname + " to file " + fileName);

		logger.debug("DbSchemaValidation = " + pilotOutputExpConfig.getDbSchemaValidation());

		TransactionStatus txStatus = startTransaction(true);

		SDDDataSet dataSet = new SDDDataSet();

		List<Taxon> taxa = null;

		List<DefinedTermBase> terms = null;

		// get data from DB

		try {

			logger.info("Retrieving data from DB");

			retrieveData(pilotOutputExpConfig, dataSet);

		} catch (Exception e) {

			logger.error("Error retrieving data");

			e.printStackTrace();

		}

		logger.info("All data retrieved");

		try {

			pilotOutputDocumentBuilder = new PilotOutputDocumentBuilder();

			File f = new File(fileName);

			FileOutputStream fos = new FileOutputStream(f);

			PrintWriter writer = new PrintWriter(new OutputStreamWriter(fos, "UTF8"), true);

			pilotOutputDocumentBuilder.marshal(dataSet, fileName);

			// TODO: Split into one file per data set member to see whether performance improves?

			logger.info("XML file written");

			logger.info("Filename is: " + fileName);

		} catch (Exception e) {

			logger.error("Marshalling error");

			e.printStackTrace();

		}

		commitTransaction(txStatus);

		return;

	}

	private void retrieveData (IExportConfigurator config, SDDDataSet sddDataSet) {

		PilotOutputExportConfigurator pilotOutputExpConfig = (PilotOutputExportConfigurator)config;

		final int MAX_ROWS = 50000;

		int numberOfRows = pilotOutputExpConfig.getMaxRows();

		// TODO:

		//CdmApplicationController appCtr = config.getCdmAppController(false, true);

		int agentRows = numberOfRows;

		int definedTermBaseRows = numberOfRows;

		int referenceBaseRows = numberOfRows;

		int taxonNameRows = numberOfRows;

		int taxonBaseRows = numberOfRows;

		int relationshipRows = numberOfRows;

		int occurrencesRows = numberOfRows;

		int mediaRows = numberOfRows;

		int featureDataRows = numberOfRows;

		int languageDataRows = numberOfRows;

		int termVocabularyRows = numberOfRows;

		int homotypicalGroupRows = numberOfRows;

		if (pilotOutputExpConfig.isDoTermVocabularies() == true) {

			if (termVocabularyRows == 0) { termVocabularyRows = MAX_ROWS; }

			logger.info("# TermVocabulary");

			sddDataSet.setTermVocabularies((List)getVocabularyService().list(null,MAX_ROWS, 0,null,null));;

		}

		if (pilotOutputExpConfig.isDoLanguageData() == true) {

			if (languageDataRows == 0) { languageDataRows = MAX_ROWS; }

			logger.info("# Representation, Language String");

			sddDataSet.setLanguageData(getTermService().getAllRepresentations(MAX_ROWS, 0));

			sddDataSet.addLanguageData(getTermService().getAllLanguageStrings(MAX_ROWS, 0));

		}

		if (pilotOutputExpConfig.isDoTerms() == true) {

			if (definedTermBaseRows == 0) { definedTermBaseRows = getTermService().count(DefinedTermBase.class); }

			logger.info("# DefinedTermBase: " + definedTermBaseRows);

			sddDataSet.setTerms(getTermService().list(null,definedTermBaseRows, 0,null,null));

		}

		if (pilotOutputExpConfig.isDoAuthors() == true) {

			if (agentRows == 0) { agentRows = getAgentService().count(AgentBase.class); }

			logger.info("# Agents: " + agentRows);

			//logger.info("    # Team: " + getAgentService().count(Team.class));

			sddDataSet.setAgents(getAgentService().list(null,agentRows, 0,null,null));

		}

		if (pilotOutputExpConfig.getDoReferences() != IExportConfigurator.DO_REFERENCES.NONE) {

			if (referenceBaseRows == 0) { referenceBaseRows = getReferenceService().count(Reference.class); }

			logger.info("# Reference: " + referenceBaseRows);

			sddDataSet.setReferences(getReferenceService().list(null,referenceBaseRows, 0,null,null));

		}

		if (pilotOutputExpConfig.isDoTaxonNames() == true) {

			if (taxonNameRows == 0) { taxonNameRows = getNameService().count(TaxonName.class); }

			logger.info("# TaxonName: " + taxonNameRows);

			//logger.info("    # Taxon: " + getNameService().count(BotanicalName.class));

			sddDataSet.setTaxonomicNames(getNameService().list(null,taxonNameRows, 0,null,null));

		}

		if (pilotOutputExpConfig.isDoHomotypicalGroups() == true) {

			if (homotypicalGroupRows == 0) { homotypicalGroupRows = MAX_ROWS; }

			logger.info("# Homotypical Groups");

			sddDataSet.setHomotypicalGroups(getNameService().getAllHomotypicalGroups(homotypicalGroupRows, 0));

		}

		if (pilotOutputExpConfig.isDoTaxa() == true) {

			if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); }

			logger.info("# TaxonBase: " + taxonBaseRows);

//			dataSet.setTaxa(new ArrayList<Taxon>());

//			dataSet.setSynonyms(new ArrayList<Synonym>());

			List<TaxonBase> tb = getTaxonService().list(null,taxonBaseRows, 0,null,null);

			for (TaxonBase taxonBase : tb) {

				if (taxonBase instanceof Taxon) {

					sddDataSet.addTaxon((Taxon)taxonBase);

				} else if (taxonBase instanceof Synonym) {

					sddDataSet.addSynonym((Synonym)taxonBase);

				} else {

					logger.error("entry of wrong type: " + taxonBase.toString());

				}

			}

		}

		// TODO:

		// retrieve taxa and synonyms separately

		// need correct count for taxa and synonyms

//		if (taxonBaseRows == 0) { taxonBaseRows = getTaxonService().count(TaxonBase.class); }

//		logger.info("# Synonym: " + taxonBaseRows);

//		dataSet.setSynonyms(new ArrayList<Synonym>());

//		dataSet.setSynonyms(getTaxonService().getAllSynonyms(taxonBaseRows, 0));

//

//		if (pilotOutputExpConfig.isDoRelTaxa() == true) {

//			if (relationshipRows == 0) { relationshipRows = MAX_ROWS; }

//			logger.info("# Relationships");

//			List<RelationshipBase> relationList = getTaxonService().getAllRelationships(relationshipRows, 0);

//			Set<RelationshipBase> relationSet = new HashSet<RelationshipBase>(relationList);

//			sddDataSet.setRelationships(relationSet);

//		}

		if (pilotOutputExpConfig.isDoReferencedEntities() == true) {

			logger.info("# Referenced Entities");

			sddDataSet.setReferencedEntities(getNameService().getAllNomenclaturalStatus(MAX_ROWS, 0));

			sddDataSet.addSourcedEntities(getNameService().getAllTypeDesignations(MAX_ROWS, 0));

		}

		if (pilotOutputExpConfig.isDoOccurrence() == true) {

			if (occurrencesRows == 0) { occurrencesRows = getOccurrenceService().count(SpecimenOrObservationBase.class); }

			logger.info("# SpecimenOrObservationBase: " + occurrencesRows);

			sddDataSet.setOccurrences(getOccurrenceService().list(null,occurrencesRows, 0,null,null));

		}

		if (pilotOutputExpConfig.isDoMedia() == true) {

			if (mediaRows == 0) { mediaRows = MAX_ROWS; }

			logger.info("# Media");

			sddDataSet.setMedia(getMediaService().list(null,mediaRows, 0,null,null));

//			dataSet.addMedia(getMediaService().getAllMediaRepresentations(mediaRows, 0));

//			dataSet.addMedia(getMediaService().getAllMediaRepresentationParts(mediaRows, 0));

		}

		if (pilotOutputExpConfig.isDoFeatureData() == true) {

			if (featureDataRows == 0) { featureDataRows = MAX_ROWS; }

			logger.info("# Feature Tree, Feature Node");

			sddDataSet.setFeatureData(getTermNodeService().list(TermType.Feature,null,null,null,null));

			sddDataSet.addFeatureData(getTermTreeService().list(TermType.Feature,null,null,null,null));

		}

	}

	@Override

	protected boolean doCheck(PilotOutputExportState state) {

		boolean result = true;

		logger.warn("No check implemented for Jaxb export");

		return result;

	}

	@Override

	protected boolean isIgnore(PilotOutputExportState state) {

		return false;

	}

    @Override

    public byte[] getByteArray() {

        // TODO Auto-generated method stub

        return null;

    }

}