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.io.IOException;

import java.io.InputStream;

import java.io.InputStreamReader;

import java.io.Reader;

import java.util.Arrays;

import java.util.HashMap;

import java.util.List;

import java.util.Map;

import java.util.Set;

import java.util.UUID;

import org.apache.log4j.Logger;

import org.springframework.security.core.GrantedAuthority;

import org.springframework.transaction.TransactionStatus;

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

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

import eu.etaxonomy.cdm.api.service.IGroupService;

import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution;

import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution.AggregationMode;

import eu.etaxonomy.cdm.api.service.pager.Pager;

import eu.etaxonomy.cdm.app.common.CdmDestinations;

import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor;

import eu.etaxonomy.cdm.database.DbSchemaValidation;

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.ext.geo.IEditGeoService;

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.agent.Person;

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

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

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

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

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

import eu.etaxonomy.cdm.model.location.NamedArea;

import eu.etaxonomy.cdm.model.location.NamedAreaLevel;

import eu.etaxonomy.cdm.model.location.NamedAreaType;

import eu.etaxonomy.cdm.model.metadata.CdmPreference;

import eu.etaxonomy.cdm.model.metadata.PreferencePredicate;

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

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

import eu.etaxonomy.cdm.model.taxon.Taxon;

import eu.etaxonomy.cdm.model.taxon.TaxonNode;

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

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

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

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

import eu.etaxonomy.cdm.persistence.hibernate.permission.Role;

import eu.etaxonomy.cdm.persistence.query.MatchMode;

import eu.etaxonomy.cdm.persistence.query.OrderHint;

/**

 * 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_Pub2();

	static final Source berlinModelSource = BerlinModelSources.euroMed_BGBM42();

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

//

    static final ICdmDataSource cdmDestination = CdmDestinations.localH2();

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

//    static final ICdmDataSource cdmDestination = CdmDestinations.cdm_local_euromed2();

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

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

    //check - import

    static final CHECK check = CHECK.CHECK_ONLY;

    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 doFacts = true;

    static final boolean doRelTaxa = true;

    static final boolean doOccurrences = true;

    static final boolean doOccurrenceSources = true;

    static final boolean doCommonNames = true;  //currently takes very long

    static final boolean doNamedAreas = true;

  //serious types do not exist in E+M except for name types which are handled in name relations

    static final boolean doTypes = false;  //serious types do not exist in E+M except for name types which are handled in name relations

    static final boolean doRunTransmissionEngine = false; // (hbm2dll == DbSchemaValidation.VALIDATE);

    //etc.

    static final boolean doMarker = false;  //no relevant markers exist

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

    boolean doPreliminaryRefDetailsWithNames = true;

    boolean logNotMatchingOldNames = false;

    boolean logMatchingNotExportedOldNames = false;  //true

    boolean checkOldNameIsSynonym = false;

    boolean includeMANsForOldNameCheck = true;

	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 2018";

	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;

	//editor - import

	static final EDITOR editor = EDITOR.EDITOR_AS_EDITOR;

	//NomenclaturalCode

	static final NomenclaturalCode nomenclaturalCode = NomenclaturalCode.ICNAFP;

	//ignore null

	static final boolean ignoreNull = false;

	static final boolean switchSpeciesGroup = true;

	static boolean useClassification = true;

	static boolean isSplitTdwgCodes = false;

	static boolean useEmAreaVocabulary = true;

	private final boolean removeHttpMapsAnchor = true;

	static final String infrGenericRankAbbrev = "[unranked]";

	static final String infrSpecificRankAbbrev = "[unranked]";

	static boolean useLastScrutinyAsSec = true;

	static boolean warnForDifferingSynonymReference = false;

	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 "

					+ "   INNER JOIN PTaxon As pt1 ON pt1.PTNameFk = r.PTNameFk1 AND pt1.PTRefFk = r.PTRefFk1 "

					+ " WHERE r.RelPTaxonID NOT IN (1874890,1874959,1874932,1874793,1874956,1874971,1874902,1874696) " //Relations to unpublished Kew genus taxa of Bethulaceae which are not imported anymore, but Bethalaceae is still imported

					+ "     AND NOT (pt1.PTRefFk = 8000000 AND pt1.publishFlag = 0) ";

	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, 13, 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 =  " authorTeamId IN (SELECT drvTab.authorTeamId FROM (SELECT authorTeamId FROM v_cdm_exp_authorTeamsAll) as drvTab) ";

	static String authorFilter = " authorId IN (SELECT drvTab.authorId FROM (SELECT authorId FROM v_cdm_exp_authorsAll) as drvTab) ";

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

	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(doOccurrences ^ invers);

		config.setDoOccurrenceSources(doOccurrenceSources ^ invers);

        config.setDoCommonNames(doCommonNames ^ invers);

        config.setDoNamedAreas(doNamedAreas ^ invers);

		config.setDoMarker(doMarker);

		config.setDoUser(doUser ^ invers);

		config.setEuroMed(true);

		config.setDoSourceNumber(true);

		config.setLogNotMatchingOldNames(logNotMatchingOldNames);

		config.setLogMatchingNotExportedOldNames(logMatchingNotExportedOldNames);

		config.setCheckOldNameIsSynonym(checkOldNameIsSynonym);

		config.setIncludeMANsForOldNameCheck(includeMANsForOldNameCheck);

		config.setUseClassification(useClassification);

		config.setSourceRefUuid(BerlinModelTransformer.uuidSourceRefEuroMed);

		config.setEditor(editor);

		config.setDbSchemaValidation(hbm2dll);

		config.setUseLastScrutinyAsSec(useLastScrutinyAsSec);

		config.setWarnForDifferingSynonymReference(warnForDifferingSynonymReference);

		// maximum number of name facts to import

		config.setMaximumNumberOfNameFacts(maximumNumberOfNameFacts);

		config.setInfrGenericRankAbbrev(infrGenericRankAbbrev);

		config.setInfrSpecificRankAbbrev(infrSpecificRankAbbrev);

		config.setRemoveHttpMapsAnchor(removeHttpMapsAnchor);

		config.setDoPreliminaryRefDetailsWithNames(doPreliminaryRefDetailsWithNames);

//		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<>();

		bmImport.invoke(config);

		renameRanks(config, bmImport);

		createFeatureTree(config, bmImport);

		changeCommonNameLabel(config, bmImport);

		createUsersAndRoles(config, bmImport);

        runTransmissionEngine(config, bmImport);

        importShapefile(config, bmImport);

        createPreferences(config, bmImport);

//        markAreasAsHidden(config, bmImport);  //has been moved to BM occurrence import

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

	}

    private void createPreferences(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

        if (config.isDoUser() && (config.getCheck().isImport() )){

            ICdmRepository app = bmImport.getCdmAppController();

            //area vocs

            CdmPreference preference = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, BerlinModelTransformer.uuidVocCaucasusAreas.toString()+";" + BerlinModelTransformer.uuidVocEuroMedAreas.toString());

            preference.setAllowOverride(false);

            app.getPreferenceService().set(preference);

            //occ status list

            String status ="42946bd6-9c22-45ad-a910-7427e8f60bfd;9eb99fe6-59e2-4445-8e6a-478365bd0fa9;c3ee7048-15b7-4be1-b687-9ce9c1a669d6;643cf9d1-a5f1-4622-9837-82ef961e880b;0c54761e-4887-4788-9dfa-7190c88746e3;83eb0aa0-1a45-495a-a3ca-bf6958b74366;aeec2947-2700-4623-8e32-9e3a430569d1;ddeac4f2-d8fa-43b8-ad7e-ca13abdd32c7;310373bf-7df4-4d02-8cb3-bcc7448805fc;5c397f7b-59ef-4c11-a33c-45691ceda91b;925662c1-bb10-459a-8c53-da5a738ac770;61cee840-801e-41d8-bead-015ad866c2f1;e191e89a-a751-4b0c-b883-7f1de70915c9";

            CdmPreference statusListPref = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AvailableDistributionAreaVocabularies, status);

            statusListPref.setAllowOverride(false);

            app.getPreferenceService().set(statusListPref);

            //distr. editor activated

            CdmPreference distrEditorActive = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DistributionEditorActivated, "true");

            statusListPref.setAllowOverride(true);

            app.getPreferenceService().set(distrEditorActive);

//            //idInVoc for areas

//            CdmPreference distrEditorShowIdInVocForAreas = CdmPreference.NewTaxEditorInstance(PreferencePredicate.Sho.ShowIdInVocabulary, "true");

//            distrEditorShowIdInVocForAreas.setAllowOverride(true);

//            app.getPreferenceService().set(distrEditorShowIdInVocForAreas);

//

//            //areas sort order

//            //?? correct?

//            CdmPreference distrEditorSorted = CdmPreference.NewTaxEditorInstance(PreferencePredicate.AreasSortedByIdInVocabulary, "true");

//            distrEditorSorted.setAllowOverride(true);

//            app.getPreferenceService().set(distrEditorSorted);

//

//            //distr. status uses symbol

//            //?? correct?

//            CdmPreference distrEditorStatusUseSymbols = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSymbolForStatus, "false");

//            distrEditorStatusUseSymbols.setAllowOverride(true);

//            app.getPreferenceService().set(distrEditorStatusUseSymbols);

            //media view

            CdmPreference showMediaView = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowMediaView, "false");

            showMediaView.setAllowOverride(false);

            app.getPreferenceService().set(showMediaView);

            //multi classification

            CdmPreference multiClassification = CdmPreference.NewTaxEditorInstance(PreferencePredicate.DisableMultiClassification, "false");

            multiClassification.setAllowOverride(false);

            app.getPreferenceService().set(multiClassification);

            //taxon node wizard

            CdmPreference showTaxonNodeWizard = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowTaxonNodeWizard, "false");

            showTaxonNodeWizard.setAllowOverride(false);

            app.getPreferenceService().set(showTaxonNodeWizard);

            //import+export

            CdmPreference showImportExportMenu = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowImportExportMenu, "false");

            showImportExportMenu.setAllowOverride(true);

            app.getPreferenceService().set(showImportExportMenu);

            //show specimen

            CdmPreference showSpecimen = CdmPreference.NewTaxEditorInstance(PreferencePredicate.ShowSpecimen, "false");

            showSpecimen.setAllowOverride(false);

            app.getPreferenceService().set(showSpecimen);

        }

    }

    //Rename Ranks (still needed?)

    private void renameRanks(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

        if (config.isDoTaxonNames() && (config.getCheck().isImport() )  ){

			ICdmRepository 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 definitely 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 definitely update the titleCache also

				app.getTermService().saveOrUpdate(subSectBot);

				app.commitTransaction(tx);

			} catch (Exception e) {

			    e.printStackTrace();

                logger.error("Exception in renameRanks: " + e.getMessage());

			}

		}

    }

    //create feature tree

    private void createFeatureTree(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport){

	    if (config.isDoFacts() && (config.getCheck().isImport()  )  ){

			try {

                ICdmRepository app = bmImport.getCdmAppController();

                TransactionStatus tx = app.startTransaction();

                //make feature tree

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

                tree.setTitleCache("Euro+Med Feature Tree", true);

                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);

                app.commitTransaction(tx);

            } catch (Exception e) {

                e.printStackTrace();

                logger.error("Exception in createFeatureTree: " + e.getMessage());

            }

		}

    }

    //Change common name label

    private void changeCommonNameLabel(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

	    if (config.isDoFacts() && (config.getCheck().isImport()  )  ){

	        try {

                ICdmRepository app = bmImport.getCdmAppController();

                TransactionStatus tx = app.startTransaction();

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

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

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

                app.getTermService().saveOrUpdate(commonNameFeature);

                app.commitTransaction(tx);

            } catch (Exception e) {

                e.printStackTrace();

                logger.error("Exception in changeCommonNameLabel: " + e.getMessage());

            }

	    }

    }

    //1. run transmission engine #3979

    private void runTransmissionEngine(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

        if (doRunTransmissionEngine && (config.getCheck().isImport()  )  ){

            try {

                ICdmRepository app = bmImport.getCdmAppController();

                final List<String> term_init_strategy = Arrays.asList(new String []{

                        "representations"

                });

                UUID uuidSuperAreaLevel = BerlinModelTransformer.uuidEuroMedAreaLevelFirst;

                NamedAreaLevel euroMedLevel1 = (NamedAreaLevel)app.getTermService().find(uuidSuperAreaLevel);

                Pager<NamedArea> areaPager = app.getTermService().list(

                        euroMedLevel1,

                        (NamedAreaType) null,

                        null,

                        null,

                        (List<OrderHint>) null,

                        term_init_strategy);

                TransmissionEngineDistribution transmissionEngineDistribution = (TransmissionEngineDistribution)app.getBean("transmissionEngineDistribution");

                transmissionEngineDistribution.accumulate(

                        AggregationMode.byAreasAndRanks,

                        areaPager.getRecords(),

                        Rank.UNRANKED_INFRASPECIFIC(),   //or do we even want to start from lower (UNKNOWN?)

                        Rank.GENUS(),

                        null,

                        DefaultProgressMonitor.NewInstance());

            } catch (Exception e) {

                e.printStackTrace();

                logger.error("Exception in markAreasAsHidden: " + e.getMessage());

            }

        }

    }

//    //5.Mark areas to be hidden #3979 .5

//    private void markAreasAsHidden(BerlinModelImportConfigurator config,

//            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

//

//        if (config.isDoOccurrence() && (config.getCheck().isImport())){

//	        try {

//                ICdmRepository app = bmImport.getCdmAppController();

//                TransactionStatus tx = app.startTransaction();

//

//                MarkerType hiddenAreaMarkerType = MarkerType.NewInstance("Used to hide distributions for the named areas in publications", "Hidden Area", null);

//                hiddenAreaMarkerType.setUuid(BerlinModelTransformer.uuidHiddenArea);

//                @SuppressWarnings("unchecked")

//                TermVocabulary<MarkerType> vocUserDefinedMarkerTypes = app.getVocabularyService().find(CdmImportBase.uuidUserDefinedMarkerTypeVocabulary);

//                if (vocUserDefinedMarkerTypes == null){

//                    String message = "Marker type vocabulary could not be found. Hidden areas not added.";

//                    logger.error(message);

//                    System.out.println(message);

//                }else{

//                    vocUserDefinedMarkerTypes.addTerm(hiddenAreaMarkerType);

//                    app.getVocabularyService().saveOrUpdate(vocUserDefinedMarkerTypes);

//

//                    //Add hidden area marker to Rs(C) and Rs(N)

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs);

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_B);

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_C);

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_E);

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_N);

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_K);

//                    hideArea(app, hiddenAreaMarkerType, BerlinModelTransformer.uuidRs_W);

//                 }

//                app.commitTransaction(tx);

//            } catch (Exception e) {

//                e.printStackTrace();

//                logger.error("Exception in markAreasAsHidden: " + e.getMessage());

//            }

//	    }

//    }

//

//    private void hideArea(ICdmRepository app, MarkerType hiddenAreaMarkerType, UUID areaUuid) {

//        NamedArea area = (NamedArea)app.getTermService().find(areaUuid);

//        area.addMarker(Marker.NewInstance(hiddenAreaMarkerType, true));

//        app.getTermService().saveOrUpdate(area);

//    }

    //2. import shapefile attributes #3979 .2

    private void importShapefile(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

        if (config.isDoOccurrence() && (config.getCheck().isImport())){

	       try {

	           UUID areaVocabularyUuid = BerlinModelTransformer.uuidVocEuroMedAreas;

               List<String> idSearchFields = Arrays.asList(new String[]{"EMAREA","PARENT"});

               String wmsLayerName = "euromed_2013";

               Set<UUID> areaUuidSet = null;

               ICdmRepository app = bmImport.getCdmAppController();

               IEditGeoService geoService = (IEditGeoService)app.getBean("editGeoService");

               Map<NamedArea, String> resultMap;

               try {

                   InputStream in = EuroMedActivator.class.getResourceAsStream("/euromed/euromed_2013.csv");

                   Reader reader = new InputStreamReader(in, "UTF-8");

                   resultMap = geoService.mapShapeFileToNamedAreas(

                               reader, idSearchFields , wmsLayerName , areaVocabularyUuid, areaUuidSet);

                   Map<String, String> flatResultMap = new HashMap<>(resultMap.size());

                   for(NamedArea area : resultMap.keySet()){

                       flatResultMap.put(area.getTitleCache() + " [" + area.getUuid() + "]", resultMap.get(area));

                   }

               } catch (IOException e) {

                    String message = "IOException when reading from mapping file or creating result map.";

                    logger.error(message);

                    System.out.println(message);

               }

            } catch (Exception e) {

                e.printStackTrace();

                logger.error("Exception in importShapefile: " + e.getMessage());

            }

	    }

    }

    //4. Create users and assign roles  #3979

    private void createUsersAndRoles(BerlinModelImportConfigurator config,

            CdmDefaultImport<BerlinModelImportConfigurator> bmImport) {

        try {

            if (config.isDoRelTaxa() && (config.getCheck().isImport())){

                ICdmRepository app = bmImport.getCdmAppController();

                TransactionStatus tx = app.startTransaction();

                //eraabstraube

                String eraabstraube = "e.raabstraube";

                List<User> users = app.getUserService().listByUsername(eraabstraube, MatchMode.EXACT, null, null, null, null, null);

                User userEraabStraube;

                if (users.isEmpty()){

                    userEraabStraube = User.NewInstance(eraabstraube, eraabstraube);

                }else{

                    userEraabStraube = users.get(0);

                }

                if (userEraabStraube.getPerson() == null){

                    Person eckhard = Person.NewInstance();

                    eckhard.setFamilyName("von Raab-Straube");

                    eckhard.setGivenName("Eckhard");

                    eckhard.setPrefix("Dr.");

                    userEraabStraube.setPerson(eckhard);

                }

                app.getUserService().saveOrUpdate(userEraabStraube);

                //groups

                Group groupEditor = app.getGroupService().load(Group.GROUP_EDITOR_UUID);

                groupEditor.addMember(userEraabStraube);

                app.getGroupService().saveOrUpdate(groupEditor);

                Group groupProjectManager = app.getGroupService().load(Group.GROUP_PROJECT_MANAGER_UUID);

                groupProjectManager.addMember(userEraabStraube);

                app.getGroupService().saveOrUpdate(groupProjectManager);

                String[] publishRoles = new String[]{Role.ROLE_PUBLISH.toString()};

                Group groupPublisher = checkGroup(app.getGroupService(), Group.GROUP_PUBLISHER_UUID, "Publisher", publishRoles);

                groupPublisher.addMember(userEraabStraube);

                app.getGroupService().saveOrUpdate(groupPublisher);

                UUID uuidEuroMedPlantBaseGroup = UUID.fromString("91be42ea-ad04-4458-9836-389277e773db");

                String[] emPlantBaseRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]"};

                Group euroMedPlantbase = checkGroup(app.getGroupService(), uuidEuroMedPlantBaseGroup, "Euro+Med Plantbase", emPlantBaseRoles);

                euroMedPlantbase.addMember(userEraabStraube);

                app.getGroupService().saveOrUpdate(euroMedPlantbase);

                //cichorieae-editor

                String cichorieaeEditor = "cichorieae-editor";

                app.getUserService().listByUsername(cichorieaeEditor, MatchMode.EXACT, null, null, null, null, null);

                User userCichEditor;

                if (users.isEmpty()){

                    userCichEditor = User.NewInstance(cichorieaeEditor, cichorieaeEditor);

                }else{

                    userCichEditor = users.get(0);

                }

                app.getUserService().saveOrUpdate(userCichEditor);

                //groups

                groupEditor.addMember(userCichEditor);

                app.getGroupService().saveOrUpdate(groupEditor);

                UUID uuidCichorieaeSubtree = null;

                UUID uuidCichorieae = UUID.fromString("63c7dbeb-b9a2-48b8-a75f-e3fe5e161f7c");

                Taxon cich = (Taxon)app.getTaxonService().find(uuidCichorieae);

                if (cich != null){

                    if (!cich.getTaxonNodes().isEmpty()){

                        TaxonNode cichNode = cich.getTaxonNodes().iterator().next();

                        uuidCichorieaeSubtree = cichNode.getUuid();

                    }

                }

                String[] cichorieaeRoles = new String[]{};

                if (uuidCichorieaeSubtree != null){

                    cichorieaeRoles = new String[]{"TAXONNODE.[CREATE,READ,UPDATE,DELETE]{"+uuidCichorieaeSubtree.toString()+"}"};

                }else{

                    String message = "Cichorieae node could not be found for cichorieae-editor role";

                    logger.warn(message);

                    System.out.println(message);

                }

                UUID uuidCichorieaeGroup = UUID.fromString("a630938d-dd4f-48c2-9406-91def487b11e");

                String cichorieaeGroupName = "Cichorieae";

                Group cichorieaeGroup = checkGroup(app.getGroupService(), uuidCichorieaeGroup, cichorieaeGroupName, cichorieaeRoles);

                cichorieaeGroup.addMember(userCichEditor);

                app.getGroupService().saveOrUpdate(cichorieaeGroup);

                app.commitTransaction(tx);

            }

        } catch (Exception e) {

            e.printStackTrace();

            logger.error("Exception in createUsersAndRoles: " + e.getMessage());

        }

    }

	/**

	  * copied from {@link FirstDataInserter#checkGroup}

     */

    private Group checkGroup(IGroupService groupService, UUID groupUuid, String groupName, String[] requiredAuthorities) {

        Group group = groupService.load(groupUuid);

        if(group == null){

            group = Group.NewInstance();

            group.setUuid(groupUuid);

            logger.info("New Group '" + groupName + "' created");

        }

        group.setName(groupName); // force name

        Set<GrantedAuthority> grantedAuthorities = group.getGrantedAuthorities();

        for(String a : requiredAuthorities){

            boolean isMissing = true;

            for(GrantedAuthority ga : grantedAuthorities){

                if(a.equals(ga.getAuthority())){

                    isMissing = false;

                    break;

                }

            }

            if(isMissing){

                GrantedAuthorityImpl newGa = GrantedAuthorityImpl.NewInstance(a);

                group.addGrantedAuthority(newGa);

                logger.info("New GrantedAuthority '" + a + "' added  to '" + groupName + "'");

            }

        }

        groupService.saveOrUpdate(group);

        logger.info("Check of group  '" + groupName + "' done");

        return group;

    }

	/**

	 * @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);

		}

		System.exit(0);

	}

}