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

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.io.berlinModel;
   5
   6 import java.sql.ResultSet;
   7 import java.sql.SQLException;
   8 import java.util.HashMap;
   9 import java.util.HashSet;
  10 import java.util.Map;
  11 import java.util.Set;
  12
  13 import org.apache.log4j.Logger;
  14
  15 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  16 import eu.etaxonomy.cdm.api.service.INameService;
  17 import eu.etaxonomy.cdm.io.common.IIO;
  18 import eu.etaxonomy.cdm.io.common.MapWrapper;
  19 import eu.etaxonomy.cdm.io.common.Source;
  20 import eu.etaxonomy.cdm.model.common.Annotation;
  21 import eu.etaxonomy.cdm.model.media.ImageFile;
  22 import eu.etaxonomy.cdm.model.media.Media;
  23 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  24 import eu.etaxonomy.cdm.model.name.TypeDesignationStatus;
  25 import eu.etaxonomy.cdm.model.occurrence.Specimen;
  26 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  27 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  28
  29
  30
  31 /**
  32  * @author a.mueller
  33  *
  34  */
  35 public class BerlinModelTypesIO extends BerlinModelIOBase implements IIO<BerlinModelImportConfigurator> {
  36         private static final Logger logger = Logger.getLogger(BerlinModelTypesIO.class);
  37
  38         private static int modCount = 10000;
  39
  40         public boolean check(BerlinModelImportConfigurator bmiConfig){
  41                 boolean result = true;
  42                 logger.warn("Checking for Types not yet implemented");
  43                 //result &= checkArticlesWithoutJournal(bmiConfig);
  44                 //result &= checkPartOfJournal(bmiConfig);
  45
  46                 return result;
  47         }
  48
  49         public static boolean invoke(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp,
  50                         MapWrapper<TaxonNameBase> taxonNameMap, MapWrapper<ReferenceBase> referenceMap){
  51
  52                 boolean result = true;
  53                 Set<TaxonNameBase> taxonNameStore = new HashSet<TaxonNameBase>();
  54                 Source source = bmiConfig.getSource();
  55                 INameService nameService = cdmApp.getNameService();
  56
  57                 Map<Integer, Specimen> typeMap = new HashMap<Integer, Specimen>();
  58                 String dbAttrName;
  59                 String cdmAttrName;
  60
  61                 logger.info("start makeTypes ...");
  62
  63                 boolean delete = bmiConfig.isDeleteAll();
  64
  65                 try {
  66                         //get data from database
  67                         String strQuery =
  68                                         " SELECT TypeDesignation.*, TypeStatus.Status " +
  69                                         " FROM TypeDesignation INNER JOIN" +
  70                         " TypeStatus ON TypeDesignation.TypeStatusFk = TypeStatus.TypeStatusId " +
  71                     " WHERE (1=1) ";
  72                         ResultSet rs = source.getResultSet(strQuery) ;
  73
  74                         int i = 0;
  75                         //for each reference
  76                         while (rs.next()){
  77
  78                                 if ((i++ % modCount) == 0){ logger.info("Types handled: " + (i-1));}
  79
  80                                 int typeDesignationId = rs.getInt("typeDesignationId");
  81                                 int nameId = rs.getInt("nameFk");
  82                                 int typeStatusFk = rs.getInt("typeStatusFk");
  83                                 int refFk = rs.getInt("refFk");
  84                                 String refDetail = rs.getString("refDetail");
  85                                 String status = rs.getString("Status");
  86                                 String typePhrase = rs.getString("typePhrase");
  87
  88                                 //TODO
  89                                 //TypeCache leer
  90                                 //RejectedFlag false
  91                                 //PublishFlag xxx
  92
  93
  94                                 TaxonNameBase taxonNameBase = taxonNameMap.get(nameId);
  95
  96                                 if (taxonNameBase != null){
  97                                         try{
  98                                                 TypeDesignationStatus typeDesignationStatus = BerlinModelTransformer.typeStatusId2TypeStatus(typeStatusFk);
  99                                                 ReferenceBase citation = referenceMap.get(refFk);
 100
 101                                                 Specimen specimen = Specimen.NewInstance();
 102                                                 specimen.setTitleCache(typePhrase);
 103                                                 boolean addToAllNames = true;
 104                                                 String originalNameString = null;
 105                                                 taxonNameBase.addSpecimenTypeDesignation(specimen, typeDesignationStatus, citation, refDetail, originalNameString, addToAllNames);
 106                                                 typeMap.put(typeDesignationId, specimen);
 107                                                 taxonNameStore.add(taxonNameBase);
 108
 109                                                 //TODO
 110                                                 //Update, Created, Notes, origId
 111                                                 //doIdCreatedUpdatedNotes(bmiConfig, media, rs, nameFactId);
 112
 113                                         }catch (UnknownCdmTypeException e) {
 114                                                 logger.warn("TypeStatus '" + status + "' not yet implemented");
 115                                         }
 116                                 }else{
 117                                         //TODO
 118                                         logger.warn("TaxonName for TypeDesignation " + typeDesignationId + " does not exist in store");
 119                                 }
 120                                 //put
 121                         }
 122
 123                         result &= makeFigures(typeMap, source);
 124
 125
 126                         logger.info("Names to save: " + taxonNameStore.size());
 127                         nameService.saveTaxonNameAll(taxonNameStore);
 128
 129                         logger.info("end makeTypes ...");
 130                         return result;
 131                 } catch (SQLException e) {
 132                         logger.error("SQLException:" +  e);
 133                         return false;
 134                 }
 135
 136         }
 137
 138         private static boolean makeFigures(Map<Integer, Specimen> typeMap, Source source){
 139                 try {
 140                         //get data from database
 141                         String strQuery =
 142                                         " SELECT * " +
 143                                         " FROM TypeFigure " +
 144                     " WHERE (1=1) ";
 145                         ResultSet rs = source.getResultSet(strQuery) ;
 146
 147                         int i = 0;
 148                         //for each reference
 149                         while (rs.next()){
 150
 151                                 if ((i++ % modCount) == 0){ logger.info("TypesFigures handled: " + (i-1));}
 152
 153                                 Integer typeFigureId = rs.getInt("typeFigureId");
 154                                 Integer typeDesignationFk = rs.getInt("typeDesignationFk");
 155                                 Integer collectionFk = rs.getInt("collectionFk");
 156                                 String filename = rs.getString("filename");
 157                                 String figurePhrase = rs.getString("figurePhrase");
 158
 159                                 String mimeType = null; //"image/jpg";
 160                                 String suffix = null; //"jpg";
 161                                 Media media = ImageFile.NewMediaInstance(null, null, filename, mimeType, suffix, null, null, null);
 162                                 if (figurePhrase != null) {
 163                                         media.addAnnotation(Annotation.NewDefaultLanguageInstance(figurePhrase));
 164                                 }
 165                                 Specimen typeSpecimen = typeMap.get(typeDesignationFk);
 166                                 if (typeSpecimen != null) {
 167                                         typeSpecimen.addMedia(media);
 168                                 }
 169
 170                                 //mimeType + suffix
 171                                 //TODO
 172                                 //RefFk
 173                                 //RefDetail
 174                                 //VerifiedBy
 175                                 //VerifiedWhen
 176                                 //PrefFigureFlag
 177                                 //PublishedFlag
 178                                 //etc.
 179                         }
 180                 } catch (SQLException e) {
 181                         logger.error("SQLException:" +  e);
 182                         return false;
 183                 }
 184
 185                 return true;
 186         }
 187
 188
 189 }