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.i4life.col;

import java.net.URI;

import java.util.UUID;

import org.apache.log4j.Logger;

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

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.common.events.LoggingIoObserver;

import eu.etaxonomy.cdm.io.dwca.in.DwcaDataImportConfiguratorBase.DatasetUse;

import eu.etaxonomy.cdm.io.dwca.in.DwcaImportConfigurator;

import eu.etaxonomy.cdm.io.dwca.in.IImportMapping.MappingType;

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

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

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

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

/**

 * @author a.mueller

 * @created 10.11.2011

 */

public class ColDwcaImportActivator {

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

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

//	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

	static final ImportSteps importSteps = ImportSteps.TaxaAndExtensions;

	static final UUID stateUuid = UUID.fromString("81b402d0-e2dc-462b-b1ff-2171b846fce9");

	static final URI source = dwca_col_All();

	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_col();

	static boolean isNoQuotes = true;

	//classification

	static final UUID classificationUuid = UUID.fromString("29d4011f-a6dd-4081-beb8-559ba6b84a6b");

	//default nom code is ICZN as it allows adding publication year

	static final NomenclaturalCode defaultNomCode = NomenclaturalCode.ICZN;

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	static int partitionSize = 1000;

	//config

	static DatasetUse datasetUse = DatasetUse.ORIGINAL_SOURCE;

	static boolean scientificNameIdAsOriginalSourceId = true;

	static boolean guessNomRef = true;

	private final boolean handleAllRefsAsCitation = true;

	//validate

	static boolean validateRankConsistency = false;

	//taxa

//	static final boolean doTaxa = true;

//	static final boolean doTaxonRelationships = false;

//	static final boolean doDistributionD = false;

	//deduplicate

	static final boolean doDeduplicate = false;

	//mapping type

	static final MappingType mappingType = MappingType.DatabaseMapping;

	static final String databaseMappingFile = "C:/Users/a.mueller/.cdmLibrary/log/colMapping";

	private void doImport(ICdmDataSource cdmDestination){

		//make Source

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

		config.addObserver(new LoggingIoObserver());

		config.setClassificationUuid(classificationUuid);

		config.setCheck(check);

		config.setDbSchemaValidation(importSteps.validation());

		config.setDoTaxonRelationships(importSteps.doTaxonRelations());

		config.setDoTaxa(importSteps.doTaxa());

		config.setDoExtensions(importSteps.doExtensions());

		config.setDoHigherRankRelationships(importSteps.doHigherTaxonRelations());

		config.setDoSplitRelationshipImport(importSteps.doSplitRelations());

		config.setDoLowerRankRelationships(importSteps.doLowerTaxonRelations());

		config.setDoSynonymRelationships(importSteps.doSynonymRelations());

		config.setKeepMappingForFurtherImports(importSteps.keepMapping());

		config.setMappingType(mappingType);

		config.setDatabaseMappingFile(databaseMappingFile);

		config.setStateUuid(stateUuid);

		config.setScientificNameIdAsOriginalSourceId(scientificNameIdAsOriginalSourceId);

		config.setValidateRankConsistency(validateRankConsistency);

		config.setDefaultPartitionSize(partitionSize);

		config.setNomenclaturalCode(defaultNomCode);

		config.setDatasetUse(datasetUse);

		config.setGuessNomenclaturalReferences(guessNomRef);

		config.setHandleAllRefsAsCitation(handleAllRefsAsCitation);

		config.setNoQuotes(isNoQuotes);

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

		//...

		if (true){

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

			config.setSourceReference(getSourceReference(config.getSourceReferenceTitle()));

			myImport.invoke(config);

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

		}

		//deduplicate

		if (doDeduplicate){

			ICdmApplicationConfiguration app = myImport.getCdmAppController();

			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.");

		}

	}

	private Reference<?> getSourceReference(String string) {

		Reference<?> result = ReferenceFactory.newGeneric();

		result.setTitleCache(string, true);

		return result;

	}

	//CoL

	public static URI dwca_col_All() {

	    //http://www.catalogueoflife.org/DCA_Export/

//	    URI sourceUrl = URI.create("file:////BGBM-PESIHPC/CoL/archive-complete_2015_07_02.zip");

//        sourceUrl = URI.create("file:////BGBM-PESIHPC/CoL/archive-complete_2015_07_02_test.zip");

        URI sourceUrl = URI.create("file:////BGBM-PESIHPC/CoL/2015-03-18-archive-complete.zip");

//	    URI sourceUrl = URI.create("file:////Pesiimport3/col/col_20Nov2012.zip");

        return sourceUrl;

	}

	private enum ImportSteps{

	    ALL,

	    TaxaOnly,

	    ExtensionsOnly,

	    TaxaAndExtensions,

	    TaxonRelationsOnly,

	    SynonymsOnly,

	    HigherTaxaOnly,

	    LowerTaxaOnly

	    ;

	    private DbSchemaValidation validation(){

	        if (this == ALL || this == TaxaOnly || this == TaxaAndExtensions){

	            return DbSchemaValidation.CREATE;

	        }else{

	            return DbSchemaValidation.VALIDATE;

	        }

	    }

        private boolean doTaxa(){

            return (this == ALL || this == TaxaOnly || this == TaxaAndExtensions);

        }

        private boolean doExtensions(){

            return (this == ALL || this == ExtensionsOnly || this == TaxaAndExtensions);

        }

        private boolean doTaxonRelations(){

            return (this == ALL || this == TaxonRelationsOnly || doSplitRelations());

        }

        private boolean doSplitRelations(){

            return (this == SynonymsOnly || this == HigherTaxaOnly || this == LowerTaxaOnly);

        }

        private boolean doSynonymRelations(){

            return (this == SynonymsOnly);

        }

        private boolean doHigherTaxonRelations(){

            return (this == HigherTaxaOnly);

        }

        private boolean doLowerTaxonRelations(){

            return (this == LowerTaxaOnly);

        }

        private boolean keepMapping(){

            return !(this == ALL || this == TaxonRelationsOnly);

        }

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		ColDwcaImportActivator me = new ColDwcaImportActivator();

		me.doImport(cdmDestination);

	}

}