EDIT

/**

* Copyright (C) 2009 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.database.update.v36_40;

import java.lang.reflect.Modifier;

import java.sql.SQLException;

import java.util.HashMap;

import java.util.Map;

import org.apache.log4j.Logger;

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

import eu.etaxonomy.cdm.database.ICdmDataSource;

import eu.etaxonomy.cdm.database.update.CaseType;

import eu.etaxonomy.cdm.database.update.ITermUpdaterStep;

import eu.etaxonomy.cdm.database.update.SchemaUpdaterStepBase;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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.location.ReferenceSystem;

import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;

import eu.etaxonomy.cdm.model.media.Media;

import eu.etaxonomy.cdm.model.media.Rights;

import eu.etaxonomy.cdm.model.media.RightsType;

import eu.etaxonomy.cdm.model.molecular.Amplification;

import eu.etaxonomy.cdm.model.molecular.AmplificationResult;

import eu.etaxonomy.cdm.model.molecular.Cloning;

import eu.etaxonomy.cdm.model.molecular.DnaSample;

import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;

import eu.etaxonomy.cdm.model.molecular.Primer;

import eu.etaxonomy.cdm.model.molecular.Sequence;

import eu.etaxonomy.cdm.model.molecular.SingleRead;

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

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

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

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

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

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

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

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

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

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

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

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

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

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

import eu.etaxonomy.cdm.model.occurrence.Collection;

import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;

import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;

import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;

import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;

import eu.etaxonomy.cdm.model.occurrence.FieldUnit;

import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;

import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;

import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;

import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;

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

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

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

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

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

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

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

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

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

/**

 * Updates the xxxObj_type field in Annotations, Markers, Extensions, Identifiers.

 * Not needed anymore as long as we gave up bidirectionality #5743

 *

 * @author a.mueller

 * @date 25.04.2016

 */

public class ReferencedObjTypeUpdater extends SchemaUpdaterStepBase<ReferencedObjTypeUpdater> implements ITermUpdaterStep{

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

	private static final String stepName = "Update referenced obj_type";

// **************************** STATIC METHODS ********************************/

	public static final ReferencedObjTypeUpdater NewInstance(){

		return new ReferencedObjTypeUpdater(stepName);

	}

	protected ReferencedObjTypeUpdater(String stepName) {

		super(stepName);

	}

	@Override

	public Integer invoke(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType) throws SQLException {

	    //TODO should better be read from eu.etaxonomy.cdm.model.common.package-info @AnyMetaDef

		try {

			Class<AnnotatableEntity>[] annotatableClasses = new Class[]{

			    Institution.class,

			    Person.class,

			    Team.class,

			    CategoricalData.class,

			    CommonTaxonName.class,

			    DescriptionElementSource.class,

			    Distribution.class,

			    Feature.class,

			    FeatureTree.class,

			    IndividualsAssociation.class,

			    MeasurementUnit.class,

			    MediaKey.class,

			    MultiAccessKey.class,

			    NaturalLanguageTerm.class,

			    PolytomousKey.class,

			    PresenceAbsenceTerm.class,

			    QuantitativeData.class,

			    SpecimenDescription.class,

			    State.class,

			    StatisticalMeasure.class,

			    TaxonDescription.class,

			    TaxonInteraction.class,

			    TaxonNameDescription.class,

			    TextData.class,

			    TextFormat.class,

			    WorkingSet.class,

			    Country.class,

			    NamedArea.class,

			    NamedAreaLevel.class,

			    NamedAreaType.class,

			    ReferenceSystem.class,

			    Media.class,

			    Rights.class,

			    RightsType.class,

			    Amplification.class,

			    AmplificationResult.class,

			    Cloning.class,

			    DnaSample.class,

			    PhylogeneticTree.class,

			    Primer.class,

			    Sequence.class,

			    SingleRead.class,

//			    BacterialName.class,

//			    BotanicalName.class,

//			    CultivarPlantName.class,

			    HomotypicalGroup.class,

			    HybridRelationship.class,

			    HybridRelationshipType.class,

			    NameRelationship.class,

			    NameRelationshipType.class,

			    NameTypeDesignationStatus.class,

                NameTypeDesignation.class,

			    NomenclaturalStatus.class,

			    NomenclaturalStatusType.class,

//			    NonViralName.class,

			    Rank.class,

			    SpecimenTypeDesignationStatus.class,

                SpecimenTypeDesignation.class,

//                ViralName.class,

//			    ZoologicalName.class,

                TaxonNameBase.class,

			    Collection.class,

			    DerivationEvent.class,

			    DerivationEventType.class,

			    DerivedUnit.class,

			    DeterminationEvent.class,

			    FieldUnit.class,

			    GatheringEvent.class,

			    MaterialOrMethodEvent.class,

			    MediaSpecimen.class,

			    PreservationMethod.class,

			    Reference.class,

			    Classification.class,

			    Synonym.class,

			    SynonymType.class,

			    Taxon.class,

			    TaxonNode.class,

			    TaxonNodeAgentRelation.class,

			    TaxonRelationship.class,

			    TaxonRelationshipType.class,

			    TermVocabulary.class,

			    OrderedTermVocabulary.class,

			    AnnotationType.class,

			    DefinedTermBase.class,

			    ExtensionType.class,

			    Language.class,

			    MarkerType.class,

			    OrderedTerm.class,

			    Annotation.class,

			    Identifier.class,

			    Credit.class,

			    LanguageString.class,

			    Representation.class,

			    IdentifiableSource.class

			};

			for (Class<AnnotatableEntity> annotatableClass : annotatableClasses){

			    updateSingleClass(datasource, monitor, caseType, annotatableClass);

			}

			return 0;

		} catch (Exception e) {

			monitor.warning(e.getMessage(), e);

			logger.warn(e.getMessage());

			return null;

		}

	}

    /**

     * @param datasource

     * @param monitor

     * @param caseType

     * @param annotatableClass2

     * @throws SQLException

     */

    private void updateSingleClass(ICdmDataSource datasource, IProgressMonitor monitor,

            CaseType caseType, Class<? extends AnnotatableEntity> annotatableClass) throws SQLException {

        if (IdentifiableEntity.class.isAssignableFrom(annotatableClass)){

            updateIdentifableEntitiy(datasource, monitor, caseType, (Class<IdentifiableEntity>)annotatableClass);

        }

        updateAnnotatableEntitiy(datasource, monitor, caseType, annotatableClass);

    }

    /**

     * @param datasource

     * @param monitor

     * @param caseType

     * @param annotatableClass

     * @throws SQLException

     */

    private void updateAnnotatableEntitiy(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,

            Class<? extends AnnotatableEntity> annotatableClass) throws SQLException {

        String sql, table;

        table = "Annotation";

        sql = "UPDATE @table SET annotatedObj_type = '@simpleClassName' WHERE id IN (SELECT annotations_id FROM @MnTable)";

        sql = setParameters(caseType, sql, table, annotatableClass);

        datasource.executeUpdate(sql);

        replaceAndExecute(datasource, caseType, annotatableClass, sql, table);

        table = "Marker";

        sql = "UPDATE @table SET markedObj_type = '@simpleClassName' WHERE id IN (SELECT markers_id FROM @MnTable)";

        sql = setParameters(caseType, sql, table, annotatableClass);

        datasource.executeUpdate(sql);

    }

    /**

     * @param caseType

     * @param sql

     * @param table

     * @param identifiableClass

     * @param isAudit

     * @return

     */

    private String setParameters(CaseType caseType, String sql, String table, Class<?> identifiableClass) {

        String simpleName = identifiableClass.getSimpleName();

        Class<?> tableClass = getTable(identifiableClass);

        String tableName = tableClass.getSimpleName();

        if (tableName.equals("Rights")){

            tableName = "RightsInfo";

        }

        String casedTable = caseType.transformTo(table);

        String mnTable = caseType.transformTo(tableName + "_" + table);

        return sql.replace("@table", casedTable)

                .replace("@simpleClassName", simpleName)

                .replace("@MnTable", mnTable);

    }

    /**

     * @param datasource

     * @param monitor

     * @param caseType

     * @param annotatableClass

     * @throws SQLException

     */

    private void updateIdentifableEntitiy(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,

            Class<? extends IdentifiableEntity> identifiableClass) throws SQLException {

        String sql, table;

        //credits, rights => do not have xxxObj_type field

        //, extensions, identifiers, sources

        //Extensions

        table = "Extension";

        sql = "UPDATE @table SET extendedObj_type = '@simpleClassName' WHERE id IN (SELECT extensions_id FROM @MnTable)";

        replaceAndExecute(datasource, caseType, identifiableClass, sql, table);

        //Identifier

        table = "Identifier";

        sql = "UPDATE @table SET identifiedObj_type = '@simpleClassName' WHERE id IN (SELECT identifiers_id FROM @MnTable)";

        replaceAndExecute(datasource, caseType, identifiableClass, sql, table);

        //OriginalSourceBase

        table = "OriginalSourceBase";

        sql = "UPDATE @table SET sourcedObj_type = '@simpleClassName' WHERE id IN (SELECT sources_id FROM @MnTable)";

        replaceAndExecute(datasource, caseType, identifiableClass, sql, table);

    }

    /**

     * @param datasource

     * @param caseType

     * @param annotatableClass

     * @param sql

     * @param table

     * @throws SQLException

     */

    private void replaceAndExecute(ICdmDataSource datasource, CaseType caseType,

            Class<? extends AnnotatableEntity> annotatableClass, String sql, String table) throws SQLException {

        sql = setParameters(caseType, sql, table, annotatableClass);

        datasource.executeUpdate(sql);

    }

    /**

     * @param identifiableClass

     */

    private Class<?> getTable(Class<?> clazz) {

        Class<?> spezificClass = specificClasses.get(clazz);

        if (spezificClass != null){

            return spezificClass;

        }else{

            boolean isAbstract = Modifier.isAbstract(clazz.getModifiers());

            if (isAbstract){

                return clazz;

            }else{

                Class<?> superClass = clazz.getSuperclass();

                //MappedSuperClasses

                if (superClass == EventBase.class

                        || superClass == AnnotatableEntity.class

                        || superClass == IdentifiableEntity.class

                        || superClass == RelationshipBase.class

                        || superClass == ReferencedEntityBase.class

                        || superClass == IdentifiableMediaEntity.class

                        || superClass == LanguageStringBase.class

                         ) {

                    return clazz;

                }

                return getTable(superClass);

            }

        }

    }

    private static Map<Class, Class> specificClasses = new HashMap<Class, Class>();

    static{

        specificClasses.put(TeamOrPersonBase.class, AgentBase.class);

        specificClasses.put(TermVocabulary.class, TermVocabulary.class);

        specificClasses.put(TypeDesignationStatusBase.class, DefinedTermBase.class);

        specificClasses.put(OrderedTermBase.class, DefinedTermBase.class);

        specificClasses.put(OrderedTermVocabulary.class, TermVocabulary.class);

        specificClasses.put(Rights.class, Rights.class);

        specificClasses.put(RelationshipTermBase.class, DefinedTermBase.class);

    }

}