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.berlinModelImport;

import java.util.UUID;

import org.apache.log4j.Logger;

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

import eu.etaxonomy.cdm.api.service.ITermService;

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

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportConfigurator;

import eu.etaxonomy.cdm.io.algaterra.AlgaTerraImportTransformer;

import eu.etaxonomy.cdm.io.algaterra.AlgaTerraSpecimenImportBase;

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.IImportConfigurator.EDITOR;

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

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;

/**

 * 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 AlgaTerraActivator {

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final Source berlinModelSource = BerlinModelSources.AlgaTerra();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_preview();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_algaterra_production();

	static final UUID treeUuid = UUID.fromString("1f617402-78dc-4bf1-ac77-d260600a8879");

	static final int sourceSecId = 7331;

	static final UUID sourceRefUuid = UUID.fromString("7e1a2500-93a5-40c2-ba34-0213d7822379");

	static final UUID featureTreeUuid = UUID.fromString("a970168a-36fd-4c7c-931e-87214a965c14");

	static final Object[] featureKeyList = new Integer[]{7,201,203,204,206,207}; 

	static final UUID specimenFeatureTreeUuid = UUID.fromString("ba86246e-d4d0-419f-832e-86d70b1e4bd7");

	static final boolean loginAsDefaultAdmin = true;

	static final boolean removeRestricted = true;

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	private boolean ignoreNull = true;

	private boolean includeFlatClassifications = true;

	private boolean includeAllNonMisappliedRelatedClassifications = true;

	private EDITOR editor = EDITOR.EDITOR_AS_EDITOR;

	//NomeclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;

	static String factFilter = " factCategoryFk NOT IN (7, 201, 202, 203, 204, 205, 206, 207, 208, 1000 ) ";

// ****************** 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;  

	//taxa

	static final boolean doTaxa = true;

	static final boolean doRelTaxa = true;

	static final boolean doFacts = true;

	//alga terra specific

	static final boolean ecoFacts = true;

	static final boolean doFactEcology = true;

	static final boolean doImages = true;

	static final boolean doDna = true;

	static final boolean doMorphology = false;

// ************************ NONE **************************************** //

//	//authors

//	static final boolean doAuthors = false;

//	//references

//	static final DO_REFERENCES doReferences =  DO_REFERENCES.ALL;

//	//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;

//	

//  //alga terra specific

//	static final boolean ecoFacts = true;

//	static final boolean doFactEcology = false;

//	static final boolean doImages = false;

//	static final boolean doDna = true;

//	static final boolean doMorphology = false;

	public void invoke(String[] args){

		System.out.println("Start import from BerlinModel("+ berlinModelSource.getDatabase() + ") ...");

		logger.debug("Start");

		//make BerlinModel Source

		Source source = berlinModelSource;

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

		AlgaTerraImportConfigurator config = AlgaTerraImportConfigurator.NewInstance(source,  destination);

		config.setClassificationUuid(treeUuid);

		config.setSourceSecId(sourceSecId);

		config.setNomenclaturalCode(nomenclaturalCode);

		config.setDoAuthors(doAuthors);

		config.setDoReferences(doReferences);

		config.setDoTaxonNames(doTaxonNames);

		config.setDoRelNames(doRelNames);

		config.setDoNameStatus(doNameStatus);

		config.setDoTypes(doTypes);

		config.setDoTaxa(doTaxa);

		config.setDoRelTaxa(doRelTaxa);

		config.setDoFacts(doFacts);

		config.setDoEcoFacts(ecoFacts);

		config.setDoImages(doImages);

		config.setDoFactEcology(doFactEcology);

		config.setDoDna(doDna);

		config.setDoMorphology(doMorphology);

		config.setSourceRefUuid(sourceRefUuid);

		config.setIgnoreNull(ignoreNull);

		config.setRemoveRestricted(removeRestricted);

		config.setIncludeFlatClassifications(includeFlatClassifications);

		config.setIncludeAllNonMisappliedRelatedClassifications(includeAllNonMisappliedRelatedClassifications);

		config.setFactFilter(factFilter);

		config.setDbSchemaValidation(hbm2dll);

		config.setCheck(check);

		config.setEditor(editor);

		if (loginAsDefaultAdmin){

			config.authenticateAsDefaultAdmin();

		}

		// invoke import

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

		bmImport.invoke(config);

		if (doFacts && (config.getCheck().equals(CHECK.CHECK_AND_IMPORT)  || config.getCheck().equals(CHECK.IMPORT_WITHOUT_CHECK) )   ){

			ICdmApplicationConfiguration app = bmImport.getCdmAppController();

			//make feature tree

			makeTaxonFeatureTree(config, app);

			//make specimen feature tree

			//TODO more specimen specific

			makeSpecimenFeatureTree(config, app);

		}

		System.out.println("End import from BerlinModel ("+ source.getDatabase() + ")...");

	}

	/**

	 * @param config

	 * @param app

	 */

	private void makeTaxonFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {

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

		tree.setTitleCache("AlgaTerra Taxon Feature Tree", true);

		FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());

		tree.getRoot().addChild(node);

//		node = FeatureNode.NewInstance(Feature.OBSERVATION());

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

//		

//		node = FeatureNode.NewInstance(Feature.SPECIMEN());

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

//		

//		node = FeatureNode.NewInstance(Feature.INDIVIDUALS_ASSOCIATION());

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

		//needed ??

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

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

//		//needed ??

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

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

		app.getFeatureTreeService().saveOrUpdate(tree);

	}

	/**

	 * @param config

	 * @param app

	 * @param tree

	 */

	private void makeSpecimenFeatureTree(AlgaTerraImportConfigurator config, ICdmApplicationConfiguration app) {

		ITermService termService = app.getTermService();

		FeatureTree specimenTree = FeatureTree.NewInstance(specimenFeatureTreeUuid);

//		FeatureTree specimenTree = TreeCreator.flatTree(specimenFeatureTreeUuid, config.getFeatureMap(), featureKeyList);

		specimenTree.setTitleCache("AlgaTerra Specimen Feature Tree", true);

		FeatureNode root = specimenTree.getRoot();

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

		root.addChild(imageNode);

		addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraClimate);

		FeatureNode node = FeatureNode.NewInstance(Feature.HABITAT());

		root.addChild(node);

		addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureHabitatExplanation);

		addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAlgaTerraLifeForm);

		addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureAdditionalData);

		addFeatureNodeByUuid(root, termService, AlgaTerraSpecimenImportBase.uuidFeatureSpecimenCommunity);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePH);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureConductivity);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureWaterTemperature);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSilica);

		FeatureNode nitrogenNode = makeNitrogenNode(root, termService);

		addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrate);

		addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureNitrite);

		addFeatureNodeByUuid(nitrogenNode, termService, AlgaTerraImportTransformer.uuidFeatureAmmonium);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeaturePhosphate);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOrthoPhosphate);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureNPRation);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureDIN);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSRP);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureOxygenSaturation);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCl);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureSecchiDepth);

		addFeatureNodeByUuid(root, termService, AlgaTerraImportTransformer.uuidFeatureCommunity);

		app.getFeatureTreeService().saveOrUpdate(specimenTree);

	}

	private FeatureNode makeNitrogenNode(FeatureNode root, ITermService termService) {

		Feature nFeature = Feature.NewInstance("Supra feature for all Nitrogen related subfeatures", "Nitrogen", "N");

		termService.save(nFeature);

		FeatureNode nNode = FeatureNode.NewInstance(nFeature);

		root.addChild(nNode);

		return nNode;

	}

//	private FeatureNode addFeataureNodesByUuidList(UUID[] featureUuidList, FeatureNode root, ITermService termService){

//		FeatureNode lastChild = null;

//		for (UUID featureUuid : featureUuidList){

//			addFeatureNodeByUuid(root, termService, featureUuid);

//		}

//

//		return lastChild;

//	}

	/**

	 * @param root

	 * @param termService

	 * @param featureUuid

	 */

	private void addFeatureNodeByUuid(FeatureNode root, ITermService termService, UUID featureUuid) {

		Feature feature = (Feature)termService.find(featureUuid);

		if (feature != null){

			FeatureNode child = FeatureNode.NewInstance(feature);

			root.addChild(child);	

		}

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		AlgaTerraActivator activator = new AlgaTerraActivator();

		activator.invoke(args);

	}

}