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 org.springframework.transaction.TransactionStatus;

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.berlinModel.BerlinModelTransformer;

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.DefinedTermBase;

import eu.etaxonomy.cdm.model.common.Language;

import eu.etaxonomy.cdm.model.common.Representation;

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.name.Rank;

/**

 * 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 {

	@SuppressWarnings("unused")

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

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

	static DbSchemaValidation hbm2dll = DbSchemaValidation.VALIDATE;

	static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();

//	static final Source berlinModelSource = BerlinModelSources.euroMed_PESI3();

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

	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_pesi_euromed();

//	static final ICdmDataSource cdmDestination = CdmDestinations.cdm_test_local_euromed3();

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

	static final boolean includePesiExport = false;

	static final int sourceSecId = 7000000; //500000

	static final UUID classificationUuid = UUID.fromString("314a68f9-8449-495a-91c2-92fde8bcf344");

	static final boolean useSingleClassification = true;

	static final String classificationName = "Euro+Med 2014";	

	static final UUID featureTreeUuid = UUID.fromString("6a5e1c2b-ec0d-46c8-9c7d-a2059267ffb7");

	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.CHECK_AND_IMPORT;

	//editor - import

	static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;

	//NomenclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;

	//ignore null

	static final boolean ignoreNull = true;

	static final boolean switchSpeciesGroup = true;

	static boolean useClassification = true;

	static boolean isSplitTdwgCodes = false;

	static boolean useEmAreaVocabulary = true;

	private boolean removeHttpMapsAnchor = true;

	static final String infrGenericRankAbbrev = "[unranked]";

	static final String infrSpecificRankAbbrev = "[unranked]";

	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" +

					" WHERE r.RelPTaxonID NOT IN (1883791,1883800,1883823,1883852,1883853,1883864,1883896,1883921,1883943,1883944,1883955,1883972,1884008,1884030,1884031,1884035) " + //Unpublished Kew taxa which are not imported anymore

					" ";  // AND r.RelQualifierFk =1 

	static String nameIdTable = " v_cdm_exp_namesAll ";

	static String referenceIdTable = " v_cdm_exp_refAll ";

	static String refDetailFilter =  " RefDetailID IN (SELECT RefDetailID FROM v_cdm_exp_RefDetail) ";

	static String factFilter = " factId IN ( SELECT factId FROM v_cdm_exp_factsAll WHERE FactCategoryFk NOT IN (12, 14, 249, 251))";

	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 *********************	

	boolean invers =   !(hbm2dll == DbSchemaValidation.CREATE);

	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 doTypes = false;  //serious types do not exist in E+M

	static final boolean doNameFacts = true;

	//taxa

	static final boolean doTaxa = true;

	static final boolean doRelTaxa = false;

	static final boolean doFacts = true;

	static final boolean doOccurences = true;

	static final boolean doCommonNames = true;

	//etc.

	static final boolean doMarker = true;

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

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

		//make BerlinModel Source

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

		config.setClassificationName(classificationName);

		config.setClassificationUuid(classificationUuid);

		config.setSourceSecId(sourceSecId);

		config.setNomenclaturalCode(nomenclaturalCode);

		config.setIgnoreNull(ignoreNull);

		config.setDoAuthors(doAuthors ^ invers);

		config.setDoReferences(invers ? doReferences.invers() : doReferences);

		config.setDoTaxonNames(doTaxonNames ^ invers);

		config.setDoRelNames(doRelNames ^ invers);

		config.setDoNameStatus(doNameStatus ^ invers);

		config.setDoTypes(doTypes);  //always false

		config.setDoNameFacts(doNameFacts ^ invers);

		config.setDoTaxa(doTaxa ^ invers);

		config.setDoRelTaxa(doRelTaxa ^ invers);

		config.setDoFacts(doFacts ^ invers);

		config.setDoOccurrence(doOccurences ^ invers);

		config.setDoCommonNames(doCommonNames ^ invers);

		config.setDoMarker(doMarker ^ invers);

		config.setDoUser(doUser ^ invers);

		config.setUseClassification(useClassification);

		config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);

		config.setEditor(editor);

		config.setDbSchemaValidation(hbm2dll);

		// maximum number of name facts to import

		config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);

		config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);

		config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);

		config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);

//		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.setRefDetailFilter(refDetailFilter);

		config.setCommonNameFilter(commonNameFilter);

		config.setOccurrenceFilter(occurrenceFilter);

		config.setOccurrenceSourceFilter(occurrenceSourceFilter);

		config.setWebMarkerFilter(webMarkerFilter);

		config.setUseSingleClassification(useSingleClassification);

		//TDWG codes

		config.setSplitTdwgCodes(isSplitTdwgCodes);

		config.setUseEmAreaVocabulary(useEmAreaVocabulary);

		config.setCheck(check);

		config.setEditor(editor);

		config.setRecordsPerTransaction(partitionSize);

		config.setSwitchSpeciesGroup(switchSpeciesGroup);

		// invoke import

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

		bmImport.invoke(config);

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

			ICdmApplicationConfiguration app = bmImport.getCdmAppController();

			TransactionStatus tx = app.startTransaction();

			try {

				Rank sectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());

				Representation repr = sectBot.getRepresentation(Language.ENGLISH());

				repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());

				repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());

				sectBot.setTitleCache(null, false);  //to definetely update the titleCache also

				app.getTermService().saveOrUpdate(sectBot);

				Rank subSectBot = (Rank)app.getTermService().find(Rank.SECTION_BOTANY().getUuid());

				repr = subSectBot.getRepresentation(Language.ENGLISH());

				repr.setAbbreviatedLabel(repr.getAbbreviatedLabel().replace("(bot.)", "").trim());

				repr.setLabel(repr.getLabel().replace("(Botany)", "").trim());

				subSectBot.setTitleCache(null, false);  //to definetely update the titleCache also

				app.getTermService().saveOrUpdate(subSectBot);

				app.commitTransaction(tx);

			} catch (Exception e) {

				e.printStackTrace();

			}

		}

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

			ICdmApplicationConfiguration app = bmImport.getCdmAppController();

			TransactionStatus tx = app.startTransaction();

			//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, 1); 

			FeatureNode commonNameNode = FeatureNode.NewInstance(Feature.COMMON_NAME());

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

			app.getFeatureTreeService().saveOrUpdate(tree);

			//Change common name label

			DefinedTermBase<?> commonNameFeature = app.getTermService().find(Feature.COMMON_NAME().getUuid());

			commonNameFeature.setLabel("Common Names", Language.ENGLISH());

			commonNameFeature.setTitleCache(null, false);  //to definetely update the titleCache also

			app.getTermService().saveOrUpdate(commonNameFeature);

			app.commitTransaction(tx);

		}

		if (config.isDoRelTaxa()){

		}

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

	}

	/**

	 * @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);

		if (includePesiExport){

			//not available from here since E+M was moved to app-import

//			PesiExportActivatorEM exportActivator = new PesiExportActivatorEM();

//			exportActivator.doExport(cdmRepository);

		}

	}

}