cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/common/mapping/DbImportSynonymMapper.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
  16 import org.apache.log4j.Logger;
  17
  18 import eu.etaxonomy.cdm.io.common.DbImportStateBase;
  19 import eu.etaxonomy.cdm.io.common.ICdmIO;
  20 import eu.etaxonomy.cdm.model.common.CdmBase;
  21 import eu.etaxonomy.cdm.model.reference.Reference;
  22 import eu.etaxonomy.cdm.model.taxon.Synonym;
  23 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  24 import eu.etaxonomy.cdm.model.taxon.Taxon;
  25 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  26 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  27
  28 /**
  29  * @author a.mueller
  30  * @created 12.05.2009
  31  * @version 1.0
  32  */
  33 /**
  34  * @author a.mueller
  35  * @created 02.03.2010
  36  * @version 1.0
  37  * @param <CDM_BASE>
  38  * @param <STATE>
  39  */
  40 public class DbImportSynonymMapper<STATE extends DbImportStateBase<?,?>> extends DbImportMultiAttributeMapperBase<CdmBase, STATE> {
  41         private static final Logger logger = Logger.getLogger(DbImportSynonymMapper.class);
  42
  43 //******************************** FACTORY METHOD ***************************************************/
  44
  45         public static DbImportSynonymMapper<?> NewInstance(String dbFromAttribute, String dbToAttribute, String relatedObjectNamespace, String relTypeAttribute){
  46                 return new DbImportSynonymMapper(dbFromAttribute, dbToAttribute, null, relatedObjectNamespace, relTypeAttribute);
  47         }
  48
  49 //******************************* ATTRIBUTES ***************************************/
  50         private String fromAttribute;
  51         private String toAttribute;
  52 //      private TaxonRelationshipType relType;
  53         private String relatedObjectNamespace;
  54         private String citationAttribute;
  55         private String microCitationAttribute;
  56         private String relationshipTypeAttribute;
  57
  58
  59 //********************************* CONSTRUCTOR ****************************************/
  60         /**
  61          * @param relatedObjectNamespace
  62          * @param mappingImport
  63          */
  64         protected DbImportSynonymMapper(String fromAttribute, String toAttribute, TaxonRelationshipType relType, String relatedObjectNamespace, String relTypeAttribute) {
  65                 super();
  66                 //TODO make it a single attribute mapper
  67                 this.fromAttribute = fromAttribute;
  68                 this.toAttribute = toAttribute;
  69 //              this.relType = relType;
  70                 this.relatedObjectNamespace = relatedObjectNamespace;
  71                 this.relationshipTypeAttribute = relTypeAttribute;
  72                 if (relTypeAttribute != null){
  73                         logger.warn("Synonymrelationship type not yet implemented");
  74                 }
  75         }
  76
  77 //************************************ METHODS *******************************************/
  78
  79         /* (non-Javadoc)
  80          * @see eu.etaxonomy.cdm.io.common.mapping.IDbImportMapper#invoke(java.sql.ResultSet, eu.etaxonomy.cdm.model.common.CdmBase)
  81          */
  82         public CdmBase invoke(ResultSet rs, CdmBase cdmBase) throws SQLException {
  83                 STATE state = getState();
  84                 ICdmIO currentImport = state.getCurrentIO();
  85                 if (currentImport instanceof ICheckIgnoreMapper){
  86                         boolean ignoreRecord = ((ICheckIgnoreMapper)currentImport).checkIgnoreMapper(this, rs);
  87                         if (ignoreRecord){
  88                                 return cdmBase;
  89                         }
  90                 }
  91
  92                 TaxonBase fromObject = (TaxonBase)getRelatedObject(rs, fromAttribute);
  93                 TaxonBase toObject = (TaxonBase)getRelatedObject(rs, toAttribute);
  94                 String fromId = String.valueOf(rs.getObject(fromAttribute));
  95                 String toId = String.valueOf(rs.getObject(toAttribute));
  96
  97                 //TODO cast
  98                 Reference citation = (Reference)getRelatedObject(rs, citationAttribute);
  99                 String microCitation = null;
 100                 if (citationAttribute != null){
 101                         microCitation = rs.getString(microCitationAttribute);
 102                 }
 103
 104
 105                 if (fromObject == null){
 106                         String warning  = "The synonym (" + fromId + ") could not be found. Synonym not added to accepted taxon";
 107                         logger.warn(warning);
 108                         return cdmBase;
 109                 }
 110                 Synonym synonym = checkSynonymType(fromObject, fromId);
 111
 112                 if (toObject == null){
 113                         String warning  = "The accepted taxon (" + toId + ") could not be found. Synonym not added to accepted taxon";
 114                         logger.warn(warning);
 115                         return cdmBase;
 116                 }
 117                 Taxon taxon = checkTaxonType(toObject, "Accepted taxon", toId);
 118
 119                 SynonymRelationshipType relType = SynonymRelationshipType.SYNONYM_OF();
 120
 121                 taxon.addSynonym(synonym, relType, citation, microCitation);
 122                 return synonym;
 123         }
 124
 125         /**
 126          *      //TODO copied from DbImportObjectMapper. Maybe these can be merged again in future
 127          * @param rs
 128          * @param dbAttribute
 129          * @return
 130          * @throws SQLException
 131          */
 132         protected CdmBase getRelatedObject(ResultSet rs, String dbAttribute) throws SQLException {
 133                 CdmBase result = null;
 134                 if (dbAttribute != null){
 135                         Object dbValue = rs.getObject(dbAttribute);
 136                         String id = String.valueOf(dbValue);
 137                         DbImportStateBase state = importMapperHelper.getState();
 138                         result = state.getRelatedObject(relatedObjectNamespace, id);
 139                 }
 140                 return result;
 141         }
 142
 143
 144         /**
 145          * Checks if cdmBase is of type Taxon
 146          * @param fromObject
 147          */
 148         private Taxon checkTaxonType(TaxonBase taxonBase, String typeString, String id) {
 149                 if (! taxonBase.isInstanceOf(Taxon.class)){
 150                         String warning = typeString + " (" + id + ") is not of type Taxon but of type " + taxonBase.getClass().getSimpleName();
 151                         logger.warn(warning);
 152                         throw new IllegalArgumentException(warning);
 153                 }
 154                 return (taxonBase.deproxy(taxonBase, Taxon.class));
 155         }
 156
 157         /**
 158          * Checks if cdmBase is of type Synonym
 159          * @param fromObject
 160          */
 161         private Synonym checkSynonymType(CdmBase cdmBase, String id) {
 162                 if (! cdmBase.isInstanceOf(Synonym.class)){
 163                         String warning = "Synonym (" + id + ") is not of type Synonym but of type " + cdmBase.getClass().getSimpleName();
 164                         logger.warn(warning);
 165                         throw new IllegalArgumentException(warning);
 166                 }
 167                 return (cdmBase.deproxy(cdmBase, Synonym.class));
 168         }
 169
 170
 171 }