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.app.wp6.cichorieae;

import java.io.File;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

import eu.etaxonomy.cdm.api.application.ICdmRepository;

import eu.etaxonomy.cdm.app.berlinModelImport.BerlinModelSources;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;

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

import eu.etaxonomy.cdm.io.common.IImportConfigurator.CHECK;

import eu.etaxonomy.cdm.io.common.IImportConfigurator.DO_REFERENCES;

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

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

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

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

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

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

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

/**

 * TODO add the following to a wiki page:

 * HINT: If you are about to import into a mysql data base running under windows and if you wish to dump and restore the resulting data bas under another operation systen

 * you must set the mysql system variable lower_case_table_names = 0 in order to create data base with table compatible names.

 *

 *

 * @author a.mueller

 *

 */

public class TaraxacumActivator {

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

	//database validation status (create, update, validate ...)

	static DbSchemaValidation hbm2dll = DbSchemaValidation.UPDATE;

	static final Source berlinModelSource = BerlinModelSources.EDIT_Taraxacum();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2Cichorieae();

	static final UUID treeUuid = UUID.fromString("019c4b4d-736b-4d2e-883c-e3244167080a");

//	static final UUID treeUuid = UUID.fromString("00db28a7-50e1-4abc-86ec-b2a8ce870de9");

//	static final UUID treeUuid = UUID.fromString("534e190f-3339-49ba-95d9-fa27d5493e3e");

	static final int sourceSecId = 7800000;

	static final UUID featureTreeUuid = UUID.fromString("ab007336-d853-4f2f-a490-7c8232eafe7b");

	static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41};

	//TODO update for Taraxacum

	static final String mediaUrlString = "http://wp5.e-taxonomy.eu/dataportal/cichorieae/media/protolog/";

	//Mac

	//static final File mediaPath = new File("/Volumes/protolog/protolog/");

	//Windows

	//static final File mediaPath = new File("\\\\media\\editwp6\\protolog");

	// set to zero for unlimited nameFacts

	static final int maximumNumberOfNameFacts = 0;

	//check - import

	//static final CHECK check = CHECK.CHECK_ONLY;

	static final CHECK check = CHECK.CHECK_AND_IMPORT;

	//NomenclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;

	//ignore null

	static final boolean ignoreNull = true;

// **************** ALL *********************

    //authors

	static final boolean doAuthors = true;

	//references

	static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;

	//names

	static final boolean doTaxonNames = true;

	static final boolean doRelNames = true;

	static final boolean doNameStatus = true;

	static final boolean doTypes = true;

	static final boolean doNameFacts = true;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doRelTaxa = true;

	static final boolean doFacts = false;

	static final boolean doOccurences = false;

	static final boolean doCommonNames = true;

// **************** SELECTED *********************

//

//	//authors

//	static final boolean doAuthors = false;

//	//references

//	static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;

//	//names

//	static final boolean doTaxonNames = false;

//	static final boolean doRelNames = false;

//	static final boolean doNameStatus = false;

//	static final boolean doTypes = false;

//	static final boolean doNameFacts = false;

//

//	//taxa

//	static final boolean doTaxa = false;

//	static final boolean doRelTaxa = false;

//	static final boolean doFacts = false;

//	static final boolean doOccurences = false;

	/**

	 * @param args

	 */

	public ImportResult doImport(ICdmDataSource destination, DbSchemaValidation hbm2dll) {

		ImportResult success;

		logger.info("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") to " + cdmDestination.getDatabase() + " ...");

		//make BerlinModel Source

		Source source = berlinModelSource;

		BerlinModelImportConfigurator bmImportConfigurator = BerlinModelImportConfigurator.NewInstance(source,  destination);

		bmImportConfigurator.setClassificationUuid(treeUuid);

//		bmImportConfigurator.setSecUuid(secUuid);

		bmImportConfigurator.setSourceSecId(sourceSecId);

		bmImportConfigurator.setNomenclaturalCode(nomenclaturalCode);

		bmImportConfigurator.setIgnoreNull(ignoreNull);

		bmImportConfigurator.setDoAuthors(doAuthors);

		bmImportConfigurator.setDoReferences(doReferences);

		bmImportConfigurator.setDoTaxonNames(doTaxonNames);

		bmImportConfigurator.setDoRelNames(doRelNames);

		bmImportConfigurator.setDoNameStatus(doNameStatus);

		bmImportConfigurator.setDoTypes(doTypes);

		bmImportConfigurator.setDoNameFacts(doNameFacts);

		bmImportConfigurator.setDoTaxa(doTaxa);

		bmImportConfigurator.setDoRelTaxa(doRelTaxa);

		bmImportConfigurator.setDoFacts(doFacts);

		bmImportConfigurator.setDoOccurrence(doOccurences);

		bmImportConfigurator.setDoCommonNames(doCommonNames);

		bmImportConfigurator.setDbSchemaValidation(hbm2dll);

		// mediaResourceLocations

		File mediaPath = CichorieaeActivator.protologuePath;

		if ( mediaPath.exists() && mediaPath.isDirectory()){

			bmImportConfigurator.setMediaUrl(mediaUrlString);

			bmImportConfigurator.setMediaPath(mediaPath);

		}else{

			logger.warn("Could not configure mediaResourceLocations");

		}

		// maximum number of name facts to import

		bmImportConfigurator.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);

		bmImportConfigurator.setCheck(check);

		// invoke import

		CdmDefaultImport<BerlinModelImportConfigurator> bmImport = new CdmDefaultImport<BerlinModelImportConfigurator>();

		success = bmImport.invoke(bmImportConfigurator);

		if (bmImportConfigurator.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || bmImportConfigurator.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK)    ){

			ICdmRepository app = bmImport.getCdmAppController();

			TransactionStatus tx = app.startTransaction();

			//make feature tree

//			FeatureTree tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);

//			FeatureNode imageNode = FeatureNode.NewInstance(Feature.IMAGE());

//			tree.getRoot().addChild(imageNode);

//			FeatureNode distributionNode = FeatureNode.NewInstance(Feature.DISTRIBUTION());

//			FeatureNode featureNode = tree.getRoot();

//			tree.getRoot().addChild(distributionNode, featureNode.getChildCount() + 1);

//			app.getFeatureTreeService().saveOrUpdate(tree);

			mergeIntoCichorieae(app);

			app.commitTransaction(tx);

		}

		logger.info("End import from BerlinModel ("+ source.getDatabase() + ")...");

		return success;

	}

	public boolean mergeIntoCichorieae(ICdmRepository app){

		boolean success = true;

	//	String taraxTaraxacumUuidStr = "9a7bced0-fa1a-432e-9cca-57b62219cde6";

		String taraxTaraxacumUuidStr = "b86f1156-091c-494d-a9c9-c84d71058f98";

		UUID taraxTaraxacumUUID = UUID.fromString(taraxTaraxacumUuidStr);

		String cichTaraxacumUuidStr = "c946ac62-b6c6-493b-8ed9-278fa38b931a";

		UUID cichTaraxacumUUID = UUID.fromString(cichTaraxacumUuidStr);

		Taxon taraxacumInCichTaxon = (Taxon)app.getTaxonService().find(cichTaraxacumUUID);

		if (taraxacumInCichTaxon != null) {

			logger.info("Merge Taraxacum");

			Set<TaxonNode> taxonNodesInCich = taraxacumInCichTaxon.getTaxonNodes();

			TaxonNode taxonNodeInCich = null;

			TaxonNode parentNodeInCich = null;

			Taxon parentInCich = null;

			TaxonNode taxonNodeInTarax = null;

			if (taxonNodesInCich == null || taxonNodesInCich.isEmpty()) {

				logger.error("No taxon nodes found for Taraxacum in cichorieae database");

				success = false;

			} else {

				logger.info(taxonNodesInCich.size()+ " taxon node(s) found for Taraxacum in Cich DB");

				taxonNodeInCich = taxonNodesInCich.iterator().next();

				parentNodeInCich = taxonNodeInCich.getParent();

				parentInCich = parentNodeInCich.getTaxon();

			}

			Taxon taraxacumInTaraxTaxon = (Taxon)app.getTaxonService().find(taraxTaraxacumUUID);

			Set<TaxonNode> taxonNodesInTarax = taraxacumInTaraxTaxon.getTaxonNodes();

			Classification treeInTaraxacum = null;

			if (taxonNodesInTarax == null || taxonNodesInTarax.isEmpty()) {

				logger.warn("No taxon nodes found for Taraxacum in taraxacum database");

				success = false;

			}else{

				taxonNodeInTarax = taxonNodesInTarax.iterator().next();

				treeInTaraxacum = taxonNodeInTarax.getClassification();

			}

			//TODO reference

			Reference citation = null;

			String microcitation = null;

			taxonNodeInTarax = parentNodeInCich.addChildNode(taxonNodeInTarax, citation, microcitation);

			//parentNodeInCich.getClassification().addParentChild(parentInCich, taraxacumInTaraxTaxon, null, null);

			parentNodeInCich.deleteChildNode(taxonNodeInCich);

			app.getTaxonService().save(parentInCich);

			app.getTaxonService().delete(taraxacumInCichTaxon);

			try {

//				app.getClassificationService().delete(treeInTaraxacum); //throws exception

			} catch (Exception e) {

				e.printStackTrace();

				return false;

			}

		}else{

			logger.warn("Taraxacum in cichorieae not found");

			success = false;

		}

		return success;

	}

	public static void main(String[] args) {

		TaraxacumActivator ta = new TaraxacumActivator();

		ICdmDataSource destination = CdmDestinations.chooseDestination(args) != null ? CdmDestinations.chooseDestination(args) : cdmDestination;

		ta.doImport(destination, hbm2dll);

	}

}