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.vibrant;

import java.lang.reflect.Method;

import java.sql.ResultSet;

import java.sql.SQLException;

import java.util.UUID;

import org.apache.log4j.Logger;

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

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.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.common.ExtensionType;

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.taxon.TaxonBase;

/**

 * 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 EuroMedActivator {

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.CREATE;

//	static final Source berlinModelSource = BerlinModelSources.euroMed();

	static final Source berlinModelSource = BerlinModelSources.PESI3_euroMed();

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

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

	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_mysql();

	static final boolean includePesiExport = false;

	static final int sourceSecId = 7000000; //500000

	static final UUID classificationUuid = UUID.fromString("5e05ebc5-6075-45ff-81df-4cefafafa4a3");

	static final boolean useSingleClassification = true;

	//from PESI-transformer

	static UUID uuidSourceRefEuroMed = UUID.fromString("0603a84a-f024-4454-ab92-9e2ac0139126");

	static final UUID featureTreeUuid = UUID.fromString("eff345e7-0619-4ec3-955d-997c1fafffc3");

	static final Object[] featureKeyList = new Integer[]{1, 31, 4, 98, 41}; 	

	// set to zero for unlimited nameFacts

	static final int maximumNumberOfNameFacts = 0;

	static final int partitionSize = 2500;

	//check - import

	static final CHECK check = CHECK.IMPORT_WITHOUT_CHECK;

	//editor - import

	static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;

	//NomeclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;

	//ignore null

	static final boolean ignoreNull = true;

	static final boolean switchSpeciesGroup = true;

	static boolean useClassification = true;

	static String taxonTable = "v_cdm_exp_taxaAll";

	static String classificationQuery = " SELECT DISTINCT t.PTRefFk, r.RefCache FROM PTaxon t INNER JOIN Reference r ON t.PTRefFk = r.RefId WHERE t.PTRefFk = " + sourceSecId; 

	static String relPTaxonIdQuery = " SELECT r.RelPTaxonId " + 

					" FROM RelPTaxon AS r INNER JOIN v_cdm_exp_taxaDirect AS a ON r.PTNameFk2 = a.PTNameFk AND r.PTRefFk2 = a.PTRefFk ";

	static String nameIdTable = " v_cdm_exp_namesAll ";

	static String referenceIdTable = " v_cdm_exp_refAll ";

	static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll )";

	static String occurrenceFilter = " occurrenceId IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )";

	static String occurrenceSourceFilter = " occurrenceFk IN ( SELECT occurrenceId FROM v_cdm_exp_occurrenceAll )"; 

	static String commonNameFilter = " commonNameId IN ( SELECT commonNameId FROM v_cdm_exp_commonNamesAll )";

	static String webMarkerFilter = " TableNameFk <> 500 OR ( RIdentifierFk IN (SELECT RIdentifier FROM v_cdm_exp_taxaAll)) ";

	static String authorTeamFilter = null; // " authorTeamId IN (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) ";

	static String authorFilter = null;  // " authorId IN (SELECT authorId FROM v_cdm_exp_authorsAll) "; 

// **************** ALL *********************	

	static final boolean doUser = 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 doNameFacts = true;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doRelTaxa = true;

	static final boolean doFacts = true;

	static final boolean doOccurences = true;

	static final boolean doCommonNames = false;  //currently creates errors

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

//	static final boolean doUser = true;

//	//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 = false;

//	static final boolean doRelTaxa = false;

//	static final boolean doFacts = false;

//	static final boolean doOccurences = false;

//	static final boolean doCommonNames = false;

//	

//	//etc.

//	static final boolean doMarker = false;

	//always false

	static final boolean doTypes = false;  

	static final boolean doMarker = false;

	public void importEm2CDM (Source source, ICdmDataSource destination, DbSchemaValidation hbm2dll){

		System.out.println("Start import from BerlinModel("+ source.getDatabase() + ") to " + destination.getDatabase() + " ...");

		//make BerlinModel Source

		logger.warn("REMIND: Set publishFlag = 1 filter in 'v_cdm_exp_taxaDirect' view !! ");

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

		config.setClassificationUuid(classificationUuid);

		config.setSourceSecId(sourceSecId);

		config.setNomenclaturalCode(nomenclaturalCode);

		try {

			Method makeUrlMethod = this.getClass().getDeclaredMethod("makeUrlForTaxon", TaxonBase.class, ResultSet.class);

			config.setMakeUrlForTaxon(makeUrlMethod);

		} catch (Exception e) {

			e.printStackTrace();

			return;

		}

		config.setIgnoreNull(ignoreNull);

		config.setDoAuthors(doAuthors);

		config.setDoReferences(doReferences);

		config.setDoTaxonNames(doTaxonNames);

		config.setDoRelNames(doRelNames);

		config.setDoNameStatus(doNameStatus);

		config.setDoTypes(doTypes);

		config.setDoNameFacts(doNameFacts);

		config.setUseClassification(useClassification);

		config.setSourceRefUuid(uuidSourceRefEuroMed);

		config.setDoTaxa(doTaxa);

		config.setDoRelTaxa(doRelTaxa);

		config.setDoFacts(doFacts);

		config.setDoOccurrence(doOccurences);

		config.setDoCommonNames(doCommonNames);

		config.setDoMarker(doMarker);

		config.setDoUser(doUser);

		config.setEditor(editor);

		config.setDbSchemaValidation(hbm2dll);

		// maximum number of name facts to import

		config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);

//		filter

		config.setTaxonTable(taxonTable);

		config.setClassificationQuery(classificationQuery);

		config.setRelTaxaIdQuery(relPTaxonIdQuery);

		config.setNameIdTable(nameIdTable);

		config.setReferenceIdTable(referenceIdTable);

		config.setAuthorTeamFilter(authorTeamFilter);

		config.setAuthorFilter(authorFilter);

		config.setFactFilter(factFilter);

		config.setCommonNameFilter(commonNameFilter);

		config.setOccurrenceFilter(occurrenceFilter);

		config.setOccurrenceSourceFilter(occurrenceSourceFilter);

		config.setWebMarkerFilter(webMarkerFilter);

		config.setUseSingleClassification(useSingleClassification);

		config.setCheck(check);

		config.setEditor(editor);

		config.setRecordsPerTransaction(partitionSize);

		config.setSwitchSpeciesGroup(switchSpeciesGroup);

		// 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

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

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

			tree.getRoot().addChild(imageNode);

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

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

			app.getFeatureTreeService().saveOrUpdate(tree);

		}

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

		logger.warn("REMIND: Set publishFlag back to <= 1  in 'v_cdm_exp_taxaDirect' view !! ");

	}

	/**

	 * @param args

	 */

	public static void main(String[] args) {

		EuroMedActivator importActivator = new EuroMedActivator();

		Source source = berlinModelSource;

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

		importActivator.importEm2CDM(source, cdmRepository, hbm2dll);

	}

	private static final String URLbase = "http://ww2.bgbm.org/EuroPlusMed/PTaxonDetail.asp?";

	public static Method makeUrlForTaxon(TaxonBase<?> taxon, ResultSet rs){

		Method result = null;

		ExtensionType urlExtensionType = ExtensionType.URL();

		int nameFk;

		try {

			nameFk = rs.getInt("PTNameFk");

		int refFkInt = rs.getInt("PTRefFk");

			if (nameFk != 0 && refFkInt != 0){

				String url = String.format(URLbase + "NameId=%s&PTRefFk=%s",nameFk, refFkInt);

				taxon.addExtension(url, urlExtensionType);

			}else{

				logger.warn("NameFk or refFkInt is 0. Can't create url");

			}

		} catch (SQLException e) {

			logger.warn("Exception when trying to access result set for url creation.");

		}

		return result;

	}

}