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.UUID;

import org.apache.log4j.Logger;

import org.springframework.transaction.TransactionStatus;

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

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

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

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.BerlinModelImportConfigurator;

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

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

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

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

import eu.etaxonomy.cdm.model.description.Feature;

import eu.etaxonomy.cdm.model.description.FeatureNode;

import eu.etaxonomy.cdm.model.description.FeatureTree;

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

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

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

/**

 * 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.cdm_test_anahit2();

	org.h2.jdbc.JdbcSQLException h;

	static final UUID secUuid = UUID.fromString("ba7120ce-4fab-49dc-aaa4-f36276426aa8");

	static final int sourceSecId = 7700000;

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

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

	//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("\\\\Bgbm11\\Edit-WP6\\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.IMPORT_WITHOUT_CHECK;

	//NomeclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICBN;

	//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 = true;

//	static final boolean doOccurences = 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 = true;

	static final boolean doRelTaxa = false;

	static final boolean doFacts = false;

	static final boolean doOccurences = true;

	/**

	 * @param args

	 */

	public void doImport() {

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

		//make BerlinModel Source

		Source source = berlinModelSource;

		ICdmDataSource destination = cdmDestination;

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

		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.setDbSchemaValidation(hbm2dll);

		// mediaResourceLocations

		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>();

		bmImport.invoke(bmImportConfigurator);

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

			CdmApplicationController app = bmImport.getCdmApp();

			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());

			tree.getRoot().addChild(distributionNode, 2);

			app.getDescriptionService().saveFeatureTree(tree);

			mergeIntoCichorieae(app);

			app.commitTransaction(tx);

		}

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

	}

	public void mergeIntoCichorieae(CdmApplicationController app){

		String taraxTaraxacum = "2fd3283f-44e3-4ffd-9d15-bc5f7f0058cb";

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

		UUID taraxacumCichUUID = UUID.fromString(cichTaraxacum);

		Taxon taraxacumInCich = (Taxon)app.getTaxonService().findByUuid(taraxacumCichUUID);

		if (taraxacumInCich != null){

			logger.info("Merge Taraxacum");

			Taxon parent = taraxacumInCich.getTaxonomicParent();

			UUID taraxacumTaraxUUID = UUID.fromString(taraxTaraxacum);

			Taxon taraxacumInTarax = (Taxon)app.getTaxonService().findByUuid(taraxacumTaraxUUID);

			//TODO reference

			ReferenceBase citation = null;

			String microcitation =null;

			parent.addTaxonomicChild(taraxacumInTarax, citation, microcitation);

			app.getTaxonService().save(parent);

			parent.removeTaxonomicChild(taraxacumInCich);

			app.getTaxonService().delete(taraxacumInCich);

		}

	}

	public static void main(String[] args) {

		TaraxacumActivator ta = new TaraxacumActivator();

		ta.doImport();

	}

}