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.diptera;

import java.lang.reflect.Method;

import java.util.UUID;

import org.apache.commons.lang3.StringUtils;

import org.apache.log4j.Logger;

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

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.in.BerlinModelImportConfigurator;

import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport.PublishMarkerChooser;

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.ImportResult;

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

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

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

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

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

/**

 * 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 DipteraActivator {

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final Source berlinModelSource = BerlinModelSources.EDIT_Diptera();

	static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

	static final UUID secUuid = UUID.fromString("06fd671f-1226-4e3b-beca-1959b3b32e20");

	static final UUID treeUuid = UUID.fromString("1e3093f6-c761-4e96-8065-2c1334ddd0c1");

	static final int sourceSecId = 1000000;

	static final UUID featureTreeUuid = UUID.fromString("ae9615b8-bc60-4ed0-ad96-897f9226d568");

	static final Object[] featureKeyList = new Integer[]{1, 4, 5, 10, 11, 12, 99};

	static boolean useClassification = true;

	//editor - import

	static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;

	//check - import

	static final CHECK check = CHECK.CHECK_AND_IMPORT;

	//taxon publish marker

	static final PublishMarkerChooser taxonPublish = PublishMarkerChooser.NO_MARKER;

	static final boolean doDistributionParser = true;  //also run DipteraDistributionParser

	//NomenclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICZN;

//	//ignore null

	static final boolean ignoreNull = true;

	//update citations ?

	static final boolean updateCitations = true;

	//include collections and add to specimen

	static final boolean updateCollections = true;

	//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 = false; //There are no occurrence data in diptera

	static final boolean doCommonNames = false; //no common names in diptera

	//etc.

	static final boolean doMarker = true;

	static final boolean doUser = true;

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

//	//authors

//	static final boolean doAuthors = false;

//	//references

//	static final DO_REFERENCES doReferences =  DO_REFERENCES.NONE;

//	//names

//	static final boolean doTaxonNames = true;

//	static final boolean doRelNames = false;

//	static final boolean doNameStatus = false;

//	static final boolean doTypes = true;

//	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;

//

//	//etc.

//	static final boolean doMarker = false;

//	static final boolean doUser = true;

	/**

	 * @param destination

	 * @param args

	 */

	public ImportResult doImport(ICdmDataSource destination) {

		ImportResult success;

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

		//make BerlinModel Source

		Source source = berlinModelSource;

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

		bmImportConfigurator.setClassificationUuid(treeUuid);

		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.setUseClassification(useClassification);

		bmImportConfigurator.setDoTaxa(doTaxa);

		bmImportConfigurator.setDoRelTaxa(doRelTaxa);

		bmImportConfigurator.setDoFacts(doFacts);

		bmImportConfigurator.setDoOccurrence(doOccurences);

		bmImportConfigurator.setDoCommonNames(doCommonNames);

		bmImportConfigurator.setDoMarker(doMarker);

		bmImportConfigurator.setDoUser(doUser);

		bmImportConfigurator.setEditor(editor);

		bmImportConfigurator.setTaxonPublishMarker(taxonPublish);

		try {

			Method nameTypeDesignationStatusMethod = DipteraActivator.class.getDeclaredMethod("nameTypeDesignationStatueMethod", String.class);

			bmImportConfigurator.setNameTypeDesignationStatusMethod(nameTypeDesignationStatusMethod);

		} catch (Exception e) {

			e.printStackTrace();

			success = new ImportResult();

			success.addException(e);

			return success;

		}

		bmImportConfigurator.setDbSchemaValidation(hbm2dll);

		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();

			//parse distributions

			if (doDistributionParser){

				DipteraDistributionParser dipDist = new DipteraDistributionParser();

				dipDist.doDistribution(app);

			}

			//make feature tree

			app = bmImport.getCdmAppController();

			FeatureTree<Feature> tree = TreeCreator.flatTree(featureTreeUuid, bmImportConfigurator.getFeatureMap(), featureKeyList);

			// add image

			tree.getRoot().addChild(Feature.IMAGE());

			// add distribution

			tree.getRoot().addChild(Feature.DISTRIBUTION());

			app.getFeatureTreeService().saveOrUpdate(tree);

		}

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

		return success;

	}

	public static void main(String[] args) {

		ImportResult success;

		logger.debug("start");

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

		DipteraActivator me = new DipteraActivator();

		success = me.doImport(destination);

		DipteraPostImportUpdater updater = new DipteraPostImportUpdater();

		if (updateCitations){

			success = updater.updateCitations(destination);

		}

		if (updateCollections){

			success = updater.updateCollections(destination);

		}

	}

	private static NameTypeDesignationStatus nameTypeDesignationStatueMethod(String note){

		if (StringUtils.isBlank(note)){

			return null;

		}

		note = note.trim();

		if (note.equalsIgnoreCase("aut.") || note.equalsIgnoreCase("automatic")){

			return NameTypeDesignationStatus.AUTOMATIC();

		}else if (note.equalsIgnoreCase("subs. mon.") ){

			return NameTypeDesignationStatus.SUBSEQUENT_MONOTYPY();

		}else if (note.startsWith("mon.") ){

			return NameTypeDesignationStatus.MONOTYPY();

		}else if (note.startsWith("orig. des") ){

			return NameTypeDesignationStatus.ORIGINAL_DESIGNATION();

		}else if (note.startsWith("des") ){

			return NameTypeDesignationStatus.SUBSEQUENT_DESIGNATION();

		}else{

			logger.warn("NameTypeDesignationStatus could not be defined for: " + note);

			return null;

		}

	}

}