cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelTypesImport.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.berlinModel.in;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.HashMap;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21
  22 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  23 import eu.etaxonomy.cdm.io.common.ICdmIO;
  24 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  25 import eu.etaxonomy.cdm.io.common.MapWrapper;
  26 import eu.etaxonomy.cdm.io.common.Source;
  27 import eu.etaxonomy.cdm.model.common.Annotation;
  28 import eu.etaxonomy.cdm.model.media.ImageFile;
  29 import eu.etaxonomy.cdm.model.media.Media;
  30 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  31 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  32 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  33 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  34 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  35
  36 /**
  37  * @author a.mueller
  38  * @created 20.03.2008
  39  * @version 1.0
  40  */
  41 @Component
  42 public class BerlinModelTypesImport extends BerlinModelImportBase /*implements IIO<BerlinModelImportConfigurator>*/ {
  43         private static final Logger logger = Logger.getLogger(BerlinModelTypesImport.class);
  44
  45         private static int modCount = 10000;
  46
  47         public BerlinModelTypesImport(){
  48                 super();
  49         }
  50
  51         /* (non-Javadoc)
  52          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  53          */
  54         @Override
  55         protected boolean doCheck(BerlinModelImportState state){
  56                 boolean result = true;
  57                 logger.warn("Checking for Types not yet implemented");
  58                 //result &= checkArticlesWithoutJournal(bmiConfig);
  59                 //result &= checkPartOfJournal(bmiConfig);
  60
  61                 return result;
  62         }
  63
  64         /* (non-Javadoc)
  65          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  66          */
  67         @Override
  68         protected boolean doInvoke(BerlinModelImportState state){
  69
  70                 MapWrapper<TaxonNameBase> taxonNameMap = (MapWrapper<TaxonNameBase>)state.getStore(ICdmIO.TAXONNAME_STORE);
  71                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)state.getStore(ICdmIO.REFERENCE_STORE);
  72
  73                 boolean result = true;
  74                 Set<TaxonNameBase> taxonNameStore = new HashSet<TaxonNameBase>();
  75                 BerlinModelImportConfigurator config = state.getConfig();
  76                 Source source = config.getSource();
  77
  78                 Map<Integer, Specimen> typeMap = new HashMap<Integer, Specimen>();
  79
  80                 logger.info("start makeTypes ...");
  81
  82                 try {
  83                         //get data from database
  84                         String strQuery =
  85                                         " SELECT TypeDesignation.*, TypeStatus.Status " +
  86                                         " FROM TypeDesignation LEFT OUTER JOIN " +
  87                         " TypeStatus ON TypeDesignation.TypeStatusFk = TypeStatus.TypeStatusId " +
  88                     " WHERE (1=1) ";
  89                         ResultSet rs = source.getResultSet(strQuery) ;
  90
  91                         int i = 0;
  92                         //for each reference
  93                         while (rs.next()){
  94
  95                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Types handled: " + (i-1));}
  96
  97                                 int typeDesignationId = rs.getInt("typeDesignationId");
  98                                 int nameId = rs.getInt("nameFk");
  99                                 int typeStatusFk = rs.getInt("typeStatusFk");
 100                                 int refFk = rs.getInt("refFk");
 101                                 String refDetail = rs.getString("refDetail");
 102                                 String status = rs.getString("Status");
 103                                 String typePhrase = rs.getString("typePhrase");
 104
 105                                 //TODO
 106                                 boolean isNotDesignated = false;
 107
 108
 109                                 //TODO
 110                                 //TypeCache leer
 111                                 //RejectedFlag false
 112                                 //PublishFlag xxx
 113
 114
 115                                 TaxonNameBase<?,?> taxonNameBase = taxonNameMap.get(nameId);
 116
 117                                 if (taxonNameBase != null){
 118                                         try{
 119                                                 SpecimenTypeDesignationStatus typeDesignationStatus = BerlinModelTransformer.typeStatusId2TypeStatus(typeStatusFk);
 120                                                 ReferenceBase citation = referenceMap.get(refFk);
 121
 122                                                 Specimen specimen = Specimen.NewInstance();
 123                                                 specimen.setTitleCache(typePhrase);
 124                                                 boolean addToAllNames = true;
 125                                                 String originalNameString = null;
 126                                                 taxonNameBase.addSpecimenTypeDesignation(specimen, typeDesignationStatus, citation, refDetail, originalNameString, isNotDesignated, addToAllNames);
 127
 128                                                 typeMap.put(typeDesignationId, specimen);
 129                                                 taxonNameStore.add(taxonNameBase);
 130
 131                                                 //TODO
 132                                                 //Update, Created, Notes, origId
 133                                                 //doIdCreatedUpdatedNotes(bmiConfig, media, rs, nameFactId);
 134
 135                                         }catch (UnknownCdmTypeException e) {
 136                                                 logger.warn("TypeStatus '" + status + "' not yet implemented");
 137                                                 result = false;
 138                                         }
 139                                 }else{
 140                                         //TODO
 141                                         logger.warn("TaxonName for TypeDesignation " + typeDesignationId + " does not exist in store");
 142                                         result = false;
 143                                 }
 144                                 //put
 145                         }
 146
 147                         result &= makeFigures(typeMap, source);
 148
 149
 150                         logger.info("Names to save: " + taxonNameStore.size());
 151                         getNameService().saveTaxonNameAll(taxonNameStore);
 152
 153                         logger.info("end makeTypes ..." + getSuccessString(result));
 154                         return result;
 155                 } catch (SQLException e) {
 156                         logger.error("SQLException:" +  e);
 157                         return false;
 158                 }
 159
 160         }
 161
 162         private static boolean makeFigures(Map<Integer, Specimen> typeMap, Source source){
 163                 boolean success = true;
 164                 try {
 165                         //get data from database
 166                         String strQuery =
 167                                         " SELECT * " +
 168                                         " FROM TypeFigure " +
 169                     " WHERE (1=1) ";
 170                         ResultSet rs = source.getResultSet(strQuery) ;
 171
 172                         int i = 0;
 173                         //for each reference
 174                         while (rs.next()){
 175
 176                                 if ((i++ % modCount) == 0){ logger.info("TypesFigures handled: " + (i-1));}
 177
 178                                 Integer typeFigureId = rs.getInt("typeFigureId");
 179                                 Integer typeDesignationFk = rs.getInt("typeDesignationFk");
 180                                 Integer collectionFk = rs.getInt("collectionFk");
 181                                 String filename = rs.getString("filename");
 182                                 String figurePhrase = rs.getString("figurePhrase");
 183
 184                                 String mimeType = null; //"image/jpg";
 185                                 String suffix = null; //"jpg";
 186                                 Media media = ImageFile.NewMediaInstance(null, null, filename, mimeType, suffix, null, null, null);
 187                                 if (figurePhrase != null) {
 188                                         media.addAnnotation(Annotation.NewDefaultLanguageInstance(figurePhrase));
 189                                 }
 190                                 Specimen typeSpecimen = typeMap.get(typeDesignationFk);
 191                                 if (typeSpecimen != null) {
 192                                         typeSpecimen.addMedia(media);
 193                                 }
 194
 195                                 //mimeType + suffix
 196                                 //TODO
 197                                 //RefFk
 198                                 //RefDetail
 199                                 //VerifiedBy
 200                                 //VerifiedWhen
 201                                 //PrefFigureFlag
 202                                 //PublishedFlag
 203                                 //etc.
 204                         }
 205                 } catch (SQLException e) {
 206                         logger.error("SQLException:" +  e);
 207                         return false;
 208                 }
 209
 210                 return success;
 211         }
 212
 213         /* (non-Javadoc)
 214          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 215          */
 216         protected boolean isIgnore(BerlinModelImportState state){
 217                 return ! state.getConfig().isDoTypes();
 218         }
 219
 220 }