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.cuba;

import java.net.URI;

import java.util.UUID;

import org.apache.log4j.Logger;

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

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

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.common.CdmDefaultImport;

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

import eu.etaxonomy.cdm.io.cuba.CubaImportConfigurator;

import eu.etaxonomy.cdm.io.cuba.CubaTransformer;

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

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

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

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

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

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

/**

 * @author a.mueller

 * @since 04.01.2016

 */

public class CubaActivator {

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

//  static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

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

    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_cuba();

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

	static boolean invers = true;

    boolean doAsteraceae = include;

    boolean doConvolvulaceae = include;

    boolean doCyperaceae = include;

    boolean doDicotA_C = include;

    boolean doDicotD_M = include;

    boolean doDicotN_Z = include;

    boolean doEuphorbiaceae = include;

    boolean doFabaceae = include;

    boolean doGymnospermae = include;

    boolean doLamVerbenaceae = include;

    boolean doMalpighiaceae = include;

    boolean doMelastomataceae = include;

    boolean doMonocots = include;

    boolean doMyrtaceae = include;

    boolean doOrchidaceae = include;

    boolean doRubiaceae = include;

    boolean doUrticaceae = include;

    boolean doPteridophyta = !include;

    static boolean include = !invers;

	//feature tree uuid

	public static final UUID featureTreeUuid = UUID.fromString("dad6b9b5-693f-4367-a7aa-076cc9c99476");

	//classification

	static final UUID classificationUuid = UUID.fromString("5de394de-9c76-4b97-b04d-71be31c7f44b");

	private static final String classificationName = "Cuba Checklist";

	static final String sourceReferenceTitle = "Cuba Checklist Word Documents";

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	boolean doVocabularies = (hbm2dll == DbSchemaValidation.CREATE);

	static final boolean doTaxa = true;

	static final boolean doDeduplicate = false;

	static final boolean doAltFlorasSanchez2017 = true;

	static final boolean doAltFlorasFRC = true;

	static final boolean doAltFlorasFC = false;

	static final boolean doAltFlorasAS = false;

	private void doImport(ICdmDataSource cdmDestination){

	    URI source = monocots();  //just any

		//make Source

		CubaImportConfigurator config= CubaImportConfigurator.NewInstance(source, cdmDestination);

		config.setClassificationUuid(classificationUuid);

        config.setClassificationName(classificationName);

        config.setCheck(check);

//		config.setDoDistribution(doDistribution);

		config.setDoTaxa(doTaxa);

		config.setDbSchemaValidation(hbm2dll);

		config.setSourceReferenceTitle(sourceReferenceTitle);

		config.setDoVocabularies(doVocabularies);

		config.setDoAltFlorasAS(doAltFlorasAS);

		config.setDoAltFlorasFC(doAltFlorasFC);

		config.setDoAltFlorasFRC(doAltFlorasFRC);

		config.setDoAltFlorasSanchez2017(doAltFlorasSanchez2017);

		CdmDefaultImport<CubaImportConfigurator> myImport = new CdmDefaultImport<>();

		//...

        if (doAsteraceae){

            doSingleSource(asteraceae(), config, myImport, doVocabularies);

        }

        if (doConvolvulaceae){

            doSingleSource(convolvulaceae(), config, myImport, doVocabularies);

        }

        if (doCyperaceae){

            doSingleSource(cyperaceae(), config, myImport, doVocabularies);

        }

        if (doDicotA_C){

            doSingleSource(dicotA_C(), config, myImport, doVocabularies);

        }

        if (doDicotD_M){

            doSingleSource(dicotD_M(), config, myImport, doVocabularies);

        }

        if (doDicotN_Z){

            doSingleSource(dicotN_Z(), config, myImport, doVocabularies);

        }

        if (doEuphorbiaceae){

            doSingleSource(euphorbiaceae(), config, myImport, doVocabularies);

        }

        if (doFabaceae){

            doSingleSource(fabaceae(), config, myImport, doVocabularies);

        }

        if (doGymnospermae){

            doSingleSource(gymnospermae(), config, myImport, doVocabularies);

        }

        if (doLamVerbenaceae){

            doSingleSource(lamVerbenaceae(), config, myImport, doVocabularies);

        }

        if (doMalpighiaceae){

            doSingleSource(malpighiaceae(), config, myImport, doVocabularies);

        }

        if (doMelastomataceae){

            doSingleSource(melastomataceae(), config, myImport, doVocabularies);

        }

        if (doMonocots){

            doSingleSource(monocots(), config, myImport, doVocabularies);

        }

        if (doMyrtaceae){

            doSingleSource(myrtaceae(), config, myImport, doVocabularies);

        }

        if (doOrchidaceae){

            doSingleSource(orchidaceae(), config, myImport, doVocabularies);

        }

        if (doRubiaceae){

            doSingleSource(rubiaceae(), config, myImport, doVocabularies);

        }

        if (doUrticaceae){

            doSingleSource(urticaceae(), config, myImport, doVocabularies);

        }

        if (doPteridophyta){

            doSingleSource(pteridophyta(), config, myImport, doVocabularies);

        }

		//deduplicate

		if (doDeduplicate){

		    logger.warn("Start deduplication ...");

		    ICdmRepository app = myImport.getCdmAppController();

			if (app == null){

                app = CdmApplicationController.NewInstance(cdmDestination, hbm2dll, false);

            }

			int count = app.getAgentService().deduplicate(Person.class, null, null);

			logger.warn("Deduplicated " + count + " persons.");

//			count = app.getAgentService().deduplicate(Team.class, null, null);

//			logger.warn("Deduplicated " + count + " teams.");

//			count = app.getReferenceService().deduplicate(Reference.class, null, null);

//			logger.warn("Deduplicated " + count + " references.");

		}

		System.exit(0);

	}

    /**

     * @param source

     * @param config

     * @param myImport

     */

    private void doSingleSource(URI source, CubaImportConfigurator config,

            CdmDefaultImport<CubaImportConfigurator> myImport, boolean doVocabularies) {

        config.setSource(source);

        String fileName = source.toString();

        fileName = fileName.substring(fileName.lastIndexOf("/") + 1 );

        String message = "Start import from ("+ fileName + ") ...";

        System.out.println(message);

        logger.warn(message);

        config.setSourceReference(getSourceReference(fileName));

        config.setDoVocabularies(doVocabularies);

        myImport.invoke(config);

        if (doVocabularies){

            TermTree<Feature> tree = makeFeatureNodes(myImport.getCdmAppController().getTermService());

            myImport.getCdmAppController().getFeatureTreeService().saveOrUpdate(tree);

            this.doVocabularies = false;

        }

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

    }

    private final Reference inRef = ReferenceFactory.newGeneric();

	private Reference getSourceReference(String string) {

		Reference result = ReferenceFactory.newGeneric();

		result.setTitleCache(string, true);

		result.setInReference(inRef);

		inRef.setTitleCache(sourceReferenceTitle, true);

		return result;

	}

	private TermTree<Feature> makeFeatureNodes(ITermService service){

//		CyprusTransformer transformer = new CyprusTransformer();

	    TermTree<Feature> result = TermTree.NewFeatureInstance(featureTreeUuid);

		result.setTitleCache("Cuba Feature Tree", true);

		TermNode<Feature> root = result.getRoot();

		root.addChild(Feature.DISTRIBUTION());

//		Feature featurAltFam = (Feature)service.find(CubaTransformer.uuidAlternativeFamily);

//		root.addChild(featurAltFam);

	    Feature featurAltFam2 = (Feature)service.find(CubaTransformer.uuidAlternativeFamily2);

	    root.addChild(featurAltFam2);

		return result;

	}

	//Monocots

	public static URI monocots() {

	    return URI.create("file:////BGBM-PESIHPC/Cuba/Monocot.xlsx");

	}

	//Cyperaceae

	public static URI cyperaceae() {

	    return URI.create("file:////BGBM-PESIHPC/Cuba/Cyper_Poaceae.xlsx");

	}

    //Fabaceae

    public static URI fabaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Fabaceae.xlsx");

    }

    //Urticaceae

    public static URI urticaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Urticaceae.xlsx");

    }

    //Asteraceae

    public static URI asteraceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Asteraceae.xlsx");

    }

    //Convolvulaceae

    public static URI convolvulaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Convolvulaceae.xlsx");

    }

    //dicot A-C

    public static URI dicotA_C() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/dicotA_C.xlsx");

    }

    //dicot D-M

    public static URI dicotD_M() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/dicotD_M.xlsx");

    }

    //dicot N-Z

    public static URI dicotN_Z() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/dicotN_Z.xlsx");

    }

    //Euphorbiaceae

    public static URI euphorbiaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Euphorbiaceae.xlsx");

    }

    //Gymnospermae

    public static URI gymnospermae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/gymnospermae.xlsx");

    }

    //Lam.Verbenaceae

    public static URI lamVerbenaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Lam_Verbenaceae.xlsx");

    }

    //Malpighiaceae

    public static URI malpighiaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Malpighiaceae.xlsx");

    }

    //Melastomataceae

    public static URI melastomataceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Melastomataceae.xlsx");

    }

    //Myrtaceae

    public static URI myrtaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Myrtaceae.xlsx");

    }

    //Orchidaceae

    public static URI orchidaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Orchidaceae.xlsx");

    }

    //Rubiaceae

    public static URI rubiaceae() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Rubiaceae.xlsx");

    }

    //Rubiaceae

    public static URI pteridophyta() {

        return URI.create("file:////BGBM-PESIHPC/Cuba/Pteridophyta.xlsx");

    }

	/**

	 * @param args

	 */

	public static void main(String[] args) {

	    CubaActivator me = new CubaActivator();

		me.doImport(cdmDestination);

	    System.exit(0);

	}

}