cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportAnnotationMapper.java

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 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
  11 package eu.etaxonomy.cdm.io.common.mapping;
  12
  13 import java.sql.ResultSet;
  14 import java.sql.SQLException;
  15 import java.util.UUID;
  16
  17 import org.apache.log4j.Logger;
  18
  19 import eu.etaxonomy.cdm.api.service.ITermService;
  20 import eu.etaxonomy.cdm.api.service.IVocabularyService;
  21 import eu.etaxonomy.cdm.common.CdmUtils;
  22 import eu.etaxonomy.cdm.io.common.CdmImportBase;
  23 import eu.etaxonomy.cdm.io.common.DbImportStateBase;
  24 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  25 import eu.etaxonomy.cdm.model.common.Annotation;
  26 import eu.etaxonomy.cdm.model.common.AnnotationType;
  27 import eu.etaxonomy.cdm.model.common.CdmBase;
  28 import eu.etaxonomy.cdm.model.common.Language;
  29 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  30
  31 /**
  32  * This class maps a database attribute to CDM annotation added to the target class
  33  * TODO maybe this class should not inherit from DbSingleAttributeImportMapperBase
  34  * as it does not map to a single attribute
  35  * @author a.mueller
  36  * @created 01.03.2010
  37  * @version 1.0
  38  */
  39 public class DbImportAnnotationMapper extends DbSingleAttributeImportMapperBase<DbImportStateBase<?,?>, AnnotatableEntity> implements IDbImportMapper<DbImportStateBase<?,?>,AnnotatableEntity>{
  40         private static final Logger logger = Logger.getLogger(DbImportAnnotationMapper.class);
  41
  42         /**
  43          * FIXME Warning: the annotation type creation is not yet implemented
  44          * @param dbAttributeString
  45          * @param uuid
  46          * @param label
  47          * @param text
  48          * @param labelAbbrev
  49          * @return
  50          */
  51         public static DbImportAnnotationMapper NewInstance(String dbAttributeString, UUID uuid, String label, String text, String labelAbbrev){
  52                 Language language = null;
  53                 AnnotationType annotationType = null;
  54                 return new DbImportAnnotationMapper(dbAttributeString, uuid, label, text, labelAbbrev, language, annotationType);
  55         }
  56
  57         /**
  58          * * FIXME Warning: the annotation type creation is not yet implemented
  59          * @param dbAttributeString
  60          * @param uuid
  61          * @param label
  62          * @param text
  63          * @param labelAbbrev
  64          * @return
  65          */
  66         public static DbImportAnnotationMapper NewInstance(String dbAttributeString, UUID uuid, String label, String text, String labelAbbrev, Language language){
  67                 AnnotationType annotationType = null;
  68                 return new DbImportAnnotationMapper(dbAttributeString, uuid, label, text, labelAbbrev, language, annotationType);
  69         }
  70
  71         /**
  72          * @param dbAttributeString
  73          * @param annotationType
  74          * @return
  75          */
  76         public static DbImportAnnotationMapper NewInstance(String dbAttributeString, AnnotationType annotationType){
  77                 Language language = null;
  78                 return NewInstance(dbAttributeString, annotationType, language);
  79         }
  80
  81         /**
  82          * @param dbAttributeString
  83          * @param annotationType
  84          * @param language
  85          * @return
  86          */
  87         public static DbImportAnnotationMapper NewInstance(String dbAttributeString, AnnotationType annotationType, Language language){
  88                 String label = null;
  89                 String text = null;
  90                 String labelAbbrev = null;
  91                 UUID uuid = null;
  92                 return new DbImportAnnotationMapper(dbAttributeString, uuid, label, text, labelAbbrev, language, annotationType);
  93         }
  94
  95
  96         private AnnotationType annotationType;
  97         private String label;
  98         private String text;
  99         private String labelAbbrev;
 100         private UUID uuid;
 101         private Language language;
 102
 103         /**
 104          * @param dbAttributeString
 105          * @param uuid
 106          * @param label
 107          * @param text
 108          * @param labelAbbrev
 109          */
 110         private DbImportAnnotationMapper(String dbAttributeString, UUID uuid, String label, String text, String labelAbbrev, Language language, AnnotationType annotationType) {
 111                 super(dbAttributeString, dbAttributeString);
 112                 this.uuid = uuid;
 113                 this.label = label;
 114                 this.text = text;
 115                 this.labelAbbrev = labelAbbrev;
 116                 this.language = language;
 117                 this.annotationType = annotationType;
 118         }
 119
 120
 121         /* (non-Javadoc)
 122          * @see eu.etaxonomy.cdm.io.common.mapping.DbSingleAttributeImportMapperBase#initialize(eu.etaxonomy.cdm.io.common.DbImportStateBase, java.lang.Class)
 123          */
 124         @Override
 125         public void initialize(DbImportStateBase<?,?> state, Class<? extends CdmBase> destinationClass) {
 126                 importMapperHelper.initialize(state, destinationClass);
 127         }
 128
 129 //      /**
 130 //       * @param service
 131 //       * @param state
 132 //       * @param tableName
 133 //       */
 134 //      public void initialize(ITermService service, DbImportStateBase state, Class<? extends CdmBase> destinationClass) {
 135 //              importMapperHelper.initialize(state, destinationClass);
 136 //              try {
 137 //                      if (  checkDbColumnExists()){
 138 //                              if (this.annotationType == null){
 139 //                                      this.annotationType = getAnnotationType(service, uuid, label, text, labelAbbrev);
 140 //                              }
 141 //                      }else{
 142 //                              ignore = true;
 143 //                      }
 144 //              } catch (MethodNotSupportedException e) {
 145 //                      //do nothing
 146 //              }
 147 //      }
 148
 149
 150         /* (non-Javadoc)
 151          * @see eu.etaxonomy.cdm.io.common.mapping.DbSingleAttributeImportMapperBase#invoke(java.sql.ResultSet, eu.etaxonomy.cdm.model.common.CdmBase)
 152          */
 153         @Override
 154         public AnnotatableEntity invoke(ResultSet rs, AnnotatableEntity annotatableEntity) throws SQLException {
 155                 if (ignore){
 156                         return annotatableEntity;
 157                 }
 158                 String dbValue = rs.getString(getSourceAttribute());
 159                 return doInvoke(annotatableEntity, dbValue);
 160         }
 161
 162         /* (non-Javadoc)
 163          * @see eu.etaxonomy.cdm.io.common.mapping.DbSingleAttributeImportMapperBase#doInvoke(eu.etaxonomy.cdm.model.common.CdmBase, java.lang.Object)
 164          */
 165         @Override
 166         protected AnnotatableEntity doInvoke(AnnotatableEntity annotatableEntity, Object dbValue){
 167                 String strAnnotation = (String)dbValue;
 168                 if (CdmUtils.isNotEmpty(strAnnotation));{
 169                         Annotation annotation = Annotation.NewInstance(strAnnotation, annotationType, language);
 170                         if (annotatableEntity != null){
 171                                 annotatableEntity.addAnnotation(annotation);
 172                         }
 173                 }
 174                 return annotatableEntity;
 175         }
 176
 177
 178
 179
 180         /**
 181          * @param service
 182          * @param uuid
 183          * @param label
 184          * @param text
 185          * @param labelAbbrev
 186          * @return
 187          */
 188         protected AnnotationType getAnnotationType(CdmImportBase<?, ?> currentImport, UUID uuid, String label, String text, String labelAbbrev){
 189                 ITermService termService = currentImport.getTermService();
 190                 AnnotationType annotationType = (AnnotationType)termService.find(uuid);
 191                 if (annotationType == null){
 192                         annotationType = AnnotationType.NewInstance(text, label, labelAbbrev);
 193                         annotationType.setUuid(uuid);
 194                         //set vocabulary //TODO allow user defined vocabularies
 195                         UUID uuidAnnotationTypeVocabulary = UUID.fromString("ca04609b-1ba0-4d31-9c2e-aa8eb2f4e62d");
 196                         IVocabularyService vocService = currentImport.getVocabularyService();
 197                         TermVocabulary voc = vocService.find(uuidAnnotationTypeVocabulary);
 198                         if (voc != null){
 199                                 voc.addTerm(annotationType);
 200                         }else{
 201                                 logger.warn("Could not find default annotation type vocabulary. Vocabulary not set for new annotation type.");
 202                         }
 203                         //savetermService.save(annotationType);
 204                 }
 205                 return annotationType;
 206         }
 207
 208
 209         //not used
 210         /* (non-Javadoc)
 211          * @see eu.etaxonomy.cdm.io.common.CdmSingleAttributeMapperBase#getTypeClass()
 212          */
 213         public Class<String> getTypeClass(){
 214                 return String.class;
 215         }
 216
 217
 218
 219
 220
 221 }