cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/update/v36_40/ReferencedObjTypeUpdater.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2009 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10 package eu.etaxonomy.cdm.database.update.v36_40;
  11
  12 import java.lang.reflect.Modifier;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.Map;
  16
  17 import org.apache.log4j.Logger;
  18
  19 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  20 import eu.etaxonomy.cdm.database.ICdmDataSource;
  21 import eu.etaxonomy.cdm.database.update.CaseType;
  22 import eu.etaxonomy.cdm.database.update.ITermUpdaterStep;
  23 import eu.etaxonomy.cdm.database.update.SchemaUpdaterStepBase;
  24 import eu.etaxonomy.cdm.model.agent.AgentBase;
  25 import eu.etaxonomy.cdm.model.agent.Institution;
  26 import eu.etaxonomy.cdm.model.agent.Person;
  27 import eu.etaxonomy.cdm.model.agent.Team;
  28 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  29 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  30 import eu.etaxonomy.cdm.model.common.Annotation;
  31 import eu.etaxonomy.cdm.model.common.AnnotationType;
  32 import eu.etaxonomy.cdm.model.common.Credit;
  33 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  34 import eu.etaxonomy.cdm.model.common.EventBase;
  35 import eu.etaxonomy.cdm.model.common.ExtensionType;
  36 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  37 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  38 import eu.etaxonomy.cdm.model.common.Identifier;
  39 import eu.etaxonomy.cdm.model.common.Language;
  40 import eu.etaxonomy.cdm.model.common.LanguageString;
  41 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  42 import eu.etaxonomy.cdm.model.common.MarkerType;
  43 import eu.etaxonomy.cdm.model.common.OrderedTerm;
  44 import eu.etaxonomy.cdm.model.common.OrderedTermBase;
  45 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  46 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  47 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  48 import eu.etaxonomy.cdm.model.common.RelationshipTermBase;
  49 import eu.etaxonomy.cdm.model.common.Representation;
  50 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  51 import eu.etaxonomy.cdm.model.description.CategoricalData;
  52 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  53 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  54 import eu.etaxonomy.cdm.model.description.Distribution;
  55 import eu.etaxonomy.cdm.model.description.Feature;
  56 import eu.etaxonomy.cdm.model.description.FeatureTree;
  57 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  58 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  59 import eu.etaxonomy.cdm.model.description.MediaKey;
  60 import eu.etaxonomy.cdm.model.description.MultiAccessKey;
  61 import eu.etaxonomy.cdm.model.description.NaturalLanguageTerm;
  62 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  63 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  64 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  65 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  66 import eu.etaxonomy.cdm.model.description.State;
  67 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  68 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  69 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  70 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  71 import eu.etaxonomy.cdm.model.description.TextData;
  72 import eu.etaxonomy.cdm.model.description.TextFormat;
  73 import eu.etaxonomy.cdm.model.description.WorkingSet;
  74 import eu.etaxonomy.cdm.model.location.Country;
  75 import eu.etaxonomy.cdm.model.location.NamedArea;
  76 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  77 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  78 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  79 import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
  80 import eu.etaxonomy.cdm.model.media.Media;
  81 import eu.etaxonomy.cdm.model.media.Rights;
  82 import eu.etaxonomy.cdm.model.media.RightsType;
  83 import eu.etaxonomy.cdm.model.molecular.Amplification;
  84 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
  85 import eu.etaxonomy.cdm.model.molecular.Cloning;
  86 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  87 import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;
  88 import eu.etaxonomy.cdm.model.molecular.Primer;
  89 import eu.etaxonomy.cdm.model.molecular.Sequence;
  90 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  91 import eu.etaxonomy.cdm.model.name.BacterialName;
  92 import eu.etaxonomy.cdm.model.name.BotanicalName;
  93 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
  94 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  95 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  96 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  97 import eu.etaxonomy.cdm.model.name.NameRelationship;
  98 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  99 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
 100 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
 101 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 102 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 103 import eu.etaxonomy.cdm.model.name.NonViralName;
 104 import eu.etaxonomy.cdm.model.name.Rank;
 105 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
 106 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
 107 import eu.etaxonomy.cdm.model.name.TypeDesignationStatusBase;
 108 import eu.etaxonomy.cdm.model.name.ViralName;
 109 import eu.etaxonomy.cdm.model.name.ZoologicalName;
 110 import eu.etaxonomy.cdm.model.occurrence.Collection;
 111 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
 112 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
 113 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 114 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 115 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 116 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
 117 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
 118 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 119 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
 120 import eu.etaxonomy.cdm.model.reference.Reference;
 121 import eu.etaxonomy.cdm.model.taxon.Classification;
 122 import eu.etaxonomy.cdm.model.taxon.Synonym;
 123 import eu.etaxonomy.cdm.model.taxon.SynonymType;
 124 import eu.etaxonomy.cdm.model.taxon.Taxon;
 125 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
 126 import eu.etaxonomy.cdm.model.taxon.TaxonNodeAgentRelation;
 127 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 128 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 129
 130
 131 /**
 132  * Updates the xxxObj_type field in Annotations, Markers, Extensions, Identifiers.
 133  * Not needed anymore as long as we gave up bidirectionality #5743
 134  *
 135  * @author a.mueller
 136  * @date 25.04.2016
 137  */
 138 public class ReferencedObjTypeUpdater extends SchemaUpdaterStepBase<ReferencedObjTypeUpdater> implements ITermUpdaterStep{
 139         private static final Logger logger = Logger.getLogger(ReferencedObjTypeUpdater.class);
 140
 141         private static final String stepName = "Update referenced obj_type";
 142
 143 // **************************** STATIC METHODS ********************************/
 144
 145         public static final ReferencedObjTypeUpdater NewInstance(){
 146                 return new ReferencedObjTypeUpdater(stepName);
 147         }
 148
 149         protected ReferencedObjTypeUpdater(String stepName) {
 150                 super(stepName);
 151         }
 152
 153         @Override
 154         public Integer invoke(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType) throws SQLException {
 155
 156             //TODO should better be read from eu.etaxonomy.cdm.model.common.package-info @AnyMetaDef
 157                 try {
 158                         Class<AnnotatableEntity>[] annotatableClasses = new Class[]{
 159                             Institution.class,
 160                             Person.class,
 161                             Team.class,
 162                             CategoricalData.class,
 163                             CommonTaxonName.class,
 164                             DescriptionElementSource.class,
 165                             Distribution.class,
 166                             Feature.class,
 167                             FeatureTree.class,
 168                             IndividualsAssociation.class,
 169                             MeasurementUnit.class,
 170                             MediaKey.class,
 171                             MultiAccessKey.class,
 172                             NaturalLanguageTerm.class,
 173                             PolytomousKey.class,
 174                             PresenceAbsenceTerm.class,
 175                             QuantitativeData.class,
 176                             SpecimenDescription.class,
 177                             State.class,
 178                             StatisticalMeasure.class,
 179                             TaxonDescription.class,
 180                             TaxonInteraction.class,
 181                             TaxonNameDescription.class,
 182                             TextData.class,
 183                             TextFormat.class,
 184                             WorkingSet.class,
 185                             Country.class,
 186                             NamedArea.class,
 187                             NamedAreaLevel.class,
 188                             NamedAreaType.class,
 189                             ReferenceSystem.class,
 190                             Media.class,
 191                             Rights.class,
 192                             RightsType.class,
 193                             Amplification.class,
 194                             AmplificationResult.class,
 195                             Cloning.class,
 196                             DnaSample.class,
 197                             PhylogeneticTree.class,
 198                             Primer.class,
 199                             Sequence.class,
 200                             SingleRead.class,
 201                             BacterialName.class,
 202                             BotanicalName.class,
 203                             CultivarPlantName.class,
 204                             HomotypicalGroup.class,
 205                             HybridRelationship.class,
 206                             HybridRelationshipType.class,
 207                             NameRelationship.class,
 208                             NameRelationshipType.class,
 209                             NameTypeDesignationStatus.class,
 210                 NameTypeDesignation.class,
 211                             NomenclaturalStatus.class,
 212                             NomenclaturalStatusType.class,
 213                             NonViralName.class,
 214                             Rank.class,
 215                             SpecimenTypeDesignationStatus.class,
 216                 SpecimenTypeDesignation.class,
 217                 ViralName.class,
 218                             ZoologicalName.class,
 219                             Collection.class,
 220                             DerivationEvent.class,
 221                             DerivationEventType.class,
 222                             DerivedUnit.class,
 223                             DeterminationEvent.class,
 224                             FieldUnit.class,
 225                             GatheringEvent.class,
 226                             MaterialOrMethodEvent.class,
 227                             MediaSpecimen.class,
 228                             PreservationMethod.class,
 229                             Reference.class,
 230                             Classification.class,
 231                             Synonym.class,
 232                             SynonymType.class,
 233                             Taxon.class,
 234                             TaxonNode.class,
 235                             TaxonNodeAgentRelation.class,
 236                             TaxonRelationship.class,
 237                             TaxonRelationshipType.class,
 238
 239                             TermVocabulary.class,
 240                             OrderedTermVocabulary.class,
 241                             AnnotationType.class,
 242                             DefinedTermBase.class,
 243                             ExtensionType.class,
 244                             Language.class,
 245                             MarkerType.class,
 246                             OrderedTerm.class,
 247                             Annotation.class,
 248                             Identifier.class,
 249                             Credit.class,
 250                             LanguageString.class,
 251                             Representation.class,
 252                             IdentifiableSource.class
 253
 254                         };
 255
 256                         for (Class<AnnotatableEntity> annotatableClass : annotatableClasses){
 257                             updateSingleClass(datasource, monitor, caseType, annotatableClass);
 258                         }
 259
 260                         return 0;
 261
 262                 } catch (Exception e) {
 263                         monitor.warning(e.getMessage(), e);
 264                         logger.warn(e.getMessage());
 265                         return null;
 266                 }
 267         }
 268
 269     /**
 270      * @param datasource
 271      * @param monitor
 272      * @param caseType
 273      * @param annotatableClass2
 274      * @throws SQLException
 275      */
 276     private void updateSingleClass(ICdmDataSource datasource, IProgressMonitor monitor,
 277             CaseType caseType, Class<? extends AnnotatableEntity> annotatableClass) throws SQLException {
 278         if (IdentifiableEntity.class.isAssignableFrom(annotatableClass)){
 279             updateIdentifableEntitiy(datasource, monitor, caseType, (Class<IdentifiableEntity>)annotatableClass);
 280         }
 281         updateAnnotatableEntitiy(datasource, monitor, caseType, annotatableClass);
 282     }
 283
 284     /**
 285      * @param datasource
 286      * @param monitor
 287      * @param caseType
 288      * @param annotatableClass
 289      * @throws SQLException
 290      */
 291     private void updateAnnotatableEntitiy(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,
 292             Class<? extends AnnotatableEntity> annotatableClass) throws SQLException {
 293         String sql, table;
 294
 295         table = "Annotation";
 296         sql = "UPDATE @table SET annotatedObj_type = '@simpleClassName' WHERE id IN (SELECT annotations_id FROM @MnTable)";
 297         sql = setParameters(caseType, sql, table, annotatableClass);
 298         datasource.executeUpdate(sql);
 299         replaceAndExecute(datasource, caseType, annotatableClass, sql, table);
 300
 301         table = "Marker";
 302         sql = "UPDATE @table SET markedObj_type = '@simpleClassName' WHERE id IN (SELECT markers_id FROM @MnTable)";
 303         sql = setParameters(caseType, sql, table, annotatableClass);
 304         datasource.executeUpdate(sql);
 305
 306     }
 307
 308     /**
 309      * @param caseType
 310      * @param sql
 311      * @param table
 312      * @param identifiableClass
 313      * @param isAudit
 314      * @return
 315      */
 316     private String setParameters(CaseType caseType, String sql, String table, Class<?> identifiableClass) {
 317         String simpleName = identifiableClass.getSimpleName();
 318         Class<?> tableClass = getTable(identifiableClass);
 319         String tableName = tableClass.getSimpleName();
 320         if (tableName.equals("Rights")){
 321             tableName = "RightsInfo";
 322         }
 323         String casedTable = caseType.transformTo(table);
 324         String mnTable = caseType.transformTo(tableName + "_" + table);
 325         return sql.replace("@table", casedTable)
 326                 .replace("@simpleClassName", simpleName)
 327                 .replace("@MnTable", mnTable);
 328
 329     }
 330
 331     /**
 332      * @param datasource
 333      * @param monitor
 334      * @param caseType
 335      * @param annotatableClass
 336      * @throws SQLException
 337      */
 338     private void updateIdentifableEntitiy(ICdmDataSource datasource, IProgressMonitor monitor, CaseType caseType,
 339             Class<? extends IdentifiableEntity> identifiableClass) throws SQLException {
 340         String sql, table;
 341
 342         //credits, rights => do not have xxxObj_type field
 343         //, extensions, identifiers, sources
 344
 345         //Extensions
 346         table = "Extension";
 347         sql = "UPDATE @table SET extendedObj_type = '@simpleClassName' WHERE id IN (SELECT extensions_id FROM @MnTable)";
 348         replaceAndExecute(datasource, caseType, identifiableClass, sql, table);
 349
 350         //Identifier
 351         table = "Identifier";
 352         sql = "UPDATE @table SET identifiedObj_type = '@simpleClassName' WHERE id IN (SELECT identifiers_id FROM @MnTable)";
 353         replaceAndExecute(datasource, caseType, identifiableClass, sql, table);
 354
 355         //OriginalSourceBase
 356         table = "OriginalSourceBase";
 357         sql = "UPDATE @table SET sourcedObj_type = '@simpleClassName' WHERE id IN (SELECT sources_id FROM @MnTable)";
 358         replaceAndExecute(datasource, caseType, identifiableClass, sql, table);
 359
 360     }
 361
 362     /**
 363      * @param datasource
 364      * @param caseType
 365      * @param annotatableClass
 366      * @param sql
 367      * @param table
 368      * @throws SQLException
 369      */
 370     private void replaceAndExecute(ICdmDataSource datasource, CaseType caseType,
 371             Class<? extends AnnotatableEntity> annotatableClass, String sql, String table) throws SQLException {
 372         sql = setParameters(caseType, sql, table, annotatableClass);
 373         datasource.executeUpdate(sql);
 374     }
 375
 376     /**
 377      * @param identifiableClass
 378      */
 379     private Class<?> getTable(Class<?> clazz) {
 380         Class<?> spezificClass = specificClasses.get(clazz);
 381         if (spezificClass != null){
 382             return spezificClass;
 383         }else{
 384             boolean isAbstract = Modifier.isAbstract(clazz.getModifiers());
 385             if (isAbstract){
 386                 return clazz;
 387             }else{
 388                 Class<?> superClass = clazz.getSuperclass();
 389                 //MappedSuperClasses
 390                 if (superClass == EventBase.class
 391                         || superClass == AnnotatableEntity.class
 392                         || superClass == IdentifiableEntity.class
 393                         || superClass == RelationshipBase.class
 394                         || superClass == ReferencedEntityBase.class
 395                         || superClass == IdentifiableMediaEntity.class
 396                         || superClass == LanguageStringBase.class
 397                          ) {
 398                     return clazz;
 399                 }
 400                 return getTable(superClass);
 401             }
 402         }
 403     }
 404
 405     private static Map<Class, Class> specificClasses = new HashMap<Class, Class>();
 406     static{
 407         specificClasses.put(TeamOrPersonBase.class, AgentBase.class);
 408         specificClasses.put(TermVocabulary.class, TermVocabulary.class);
 409         specificClasses.put(TypeDesignationStatusBase.class, DefinedTermBase.class);
 410         specificClasses.put(OrderedTermBase.class, DefinedTermBase.class);
 411         specificClasses.put(OrderedTermVocabulary.class, TermVocabulary.class);
 412         specificClasses.put(Rights.class, Rights.class);
 413         specificClasses.put(RelationshipTermBase.class, DefinedTermBase.class);
 414
 415
 416
 417
 418     }
 419
 420 }