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

   1 package eu.etaxonomy.cdm.io.berlinModel;
   2
   3 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.*;
   4
   5 import java.sql.ResultSet;
   6 import java.sql.SQLException;
   7 import java.util.HashSet;
   8 import java.util.Set;
   9
  10 import org.apache.log4j.Logger;
  11
  12 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  13 import eu.etaxonomy.cdm.api.service.INameService;
  14 import eu.etaxonomy.cdm.api.service.IReferenceService;
  15 import eu.etaxonomy.cdm.io.source.Source;
  16 import eu.etaxonomy.cdm.model.agent.Agent;
  17 import eu.etaxonomy.cdm.model.name.BotanicalName;
  18 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  19 import eu.etaxonomy.cdm.model.name.Rank;
  20 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  21 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  22 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  23 import eu.etaxonomy.cdm.strategy.exceptions.UnknownRankException;
  24
  25 public class BerlinModelTaxonNameIO {
  26         private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameIO.class);
  27
  28         private static int modCount = 5000;
  29
  30         //TODO
  31         static boolean invokeStatus(ReferenceBase berlinModelRef, Source source, CdmApplicationController cdmApp,
  32                         boolean deleteAll, MapWrapper<TaxonNameBase> taxonNameMap,
  33                         MapWrapper<ReferenceBase> referenceMap, MapWrapper<Agent> authorMap){
  34                 return false;
  35         }
  36
  37         public static boolean invoke(ReferenceBase berlinModelRef, Source source, CdmApplicationController cdmApp,
  38                         boolean deleteAll, MapWrapper<TaxonNameBase> taxonNameMap,
  39                         MapWrapper<ReferenceBase> referenceMap, MapWrapper<Agent> authorMap){
  40
  41
  42                 String dbAttrName;
  43                 String cdmAttrName;
  44                 boolean success = true ;
  45
  46                 logger.info("start makeTaxonNames ...");
  47                 INameService nameService = cdmApp.getNameService();
  48                 boolean delete = deleteAll;
  49
  50                 try {
  51
  52
  53                         //get data from database
  54                         String strQuery =
  55                                         "SELECT Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +
  56                                 " RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +
  57                                 " RefDetail.SecondarySources, RefDetail.IdInSource " +
  58                     " FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND Name.NomRefDetailFk = RefDetail.RefDetailId AND " +
  59                         " Name.NomRefFk = RefDetail.RefFk AND Name.NomRefFk = RefDetail.RefFk" +
  60                     " WHERE (1=1) ";
  61                                         //strQuery += " AND Name.Created_When > '03.03.2004' ";
  62
  63
  64                         ResultSet rs = source.getResultSet(strQuery) ;
  65
  66                         int i = 0;
  67                         //for each reference
  68                         while (rs.next()){
  69
  70                                 if ((i++ % modCount) == 0){ logger.info("Names handled: " + (i-1));}
  71
  72                                 //create TaxonName element
  73                                 int nameId = rs.getInt("nameId");
  74                                 int rankId = rs.getInt("rankFk");
  75                                 Object nomRefFk = rs.getObject("NomRefFk");
  76
  77                                 try {
  78                                         if (logger.isDebugEnabled()){logger.debug(rankId);}
  79                                         Rank rank = BerlinModelTransformer.rankId2Rank(rankId);
  80                                         //FIXME
  81                                         //BotanicalName name = BotanicalName.NewInstance(BerlinModelTransformer.rankId2Rank(rankId));
  82                                         BotanicalName botanicalName = new BotanicalName(rank);
  83
  84                                         if (rankId < 40){
  85                                                 dbAttrName = "supraGenericName";
  86                                         }else{
  87                                                 dbAttrName = "genus";
  88                                         }
  89                                         cdmAttrName = "genusOrUninomial";
  90                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  91
  92                                         dbAttrName = "genusSubdivisionEpi";
  93                                         cdmAttrName = "infraGenericEpithet";
  94                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  95
  96                                         dbAttrName = "speciesEpi";
  97                                         cdmAttrName = "specificEpithet";
  98                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  99
 100
 101                                         dbAttrName = "infraSpeciesEpi";
 102                                         cdmAttrName = "infraSpecificEpithet";
 103                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 104
 105                                         dbAttrName = "unnamedNamePhrase";
 106                                         cdmAttrName = "appendedPhrase";
 107                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 108
 109                                         dbAttrName = "preliminaryFlag";
 110                                         cdmAttrName = "XX" + "protectedTitleCache";
 111                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 112
 113                                         dbAttrName = "HybridFormulaFlag";
 114                                         cdmAttrName = "isHybridFormula";
 115                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 116
 117                                         dbAttrName = "MonomHybFlag";
 118                                         cdmAttrName = "isMonomHybrid";
 119                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 120
 121                                         dbAttrName = "BinomHybFlag";
 122                                         cdmAttrName = "isBinomHybrid";
 123                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 124
 125                                         dbAttrName = "TrinomHybFlag";
 126                                         cdmAttrName = "isTrinomHybrid";
 127                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 128
 129                                         //botanicalName.s
 130
 131 //                                      dbAttrName = "notes";
 132 //                                      cdmAttrName = "isTrinomHybrid";
 133 //                                      ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 134
 135                                         //TODO
 136                                         //Created
 137                                         //Note
 138                                         //makeAuthorTeams
 139                                         //CultivarGroupName
 140                                         //CultivarName
 141                                         //Source_Acc
 142                                         //OrthoProjection
 143
 144                                         //Details
 145
 146                                         dbAttrName = "details";
 147                                         cdmAttrName = "nomenclaturalMicroReference";
 148                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 149
 150                                         //TODO
 151                                         //preliminaryFlag
 152
 153                                         if (referenceMap != null){
 154                                                 if (nomRefFk != null){
 155                                                         int nomRefFkInt = (Integer)nomRefFk;
 156                                                         ReferenceBase nomenclaturalReference = referenceMap.get(nomRefFkInt);
 157                                                         if (nomenclaturalReference == null){
 158                                                                 //TODO
 159                                                                 logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
 160                                                                 " was not found in reference store. Relation was not set!!");
 161                                                         }else if (! INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
 162                                                                 logger.error("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
 163                                                                 " is not assignable from INomenclaturalReference. Relation was not set!! (Class = " + nomenclaturalReference.getClass()+ ")");
 164                                                         }else{
 165                                                                 botanicalName.setNomenclaturalReference((INomenclaturalReference)nomenclaturalReference);
 166                                                         }
 167                                                 }
 168                                         }
 169
 170                                         //refId
 171                                         //TODO
 172                                         // Annotation annotation = new Annotation("Berlin Model nameId: " + String.valueOf(refId), Language.DEFAULT());
 173                                         // botanicalName.addAnnotations(annotation);
 174
 175                                         //nameId
 176                                         ImportHelper.setOriginalSource(botanicalName, berlinModelRef, nameId);
 177
 178                                         taxonNameMap.put(nameId, botanicalName);
 179
 180                                 } catch (UnknownRankException e) {
 181                                         logger.warn("Name with id " + nameId + " has unknown rankId " + rankId + " and could not be saved.");
 182                                         success = false;
 183                                 }
 184
 185                         } //while rs.hasNext()
 186                         logger.info(i + " names handled");
 187                         nameService.saveTaxonNameAll(taxonNameMap.objects());
 188
 189 //                      makeNameSpecificData(nameMap);
 190
 191                         logger.info("end makeTaxonNames ...");
 192                         return success;
 193                 } catch (SQLException e) {
 194                         logger.error("SQLException:" +  e);
 195                         return false;
 196                 }
 197
 198         }
 199
 200         public static boolean invokeRelations(ReferenceBase berlinModelRef, Source source, CdmApplicationController cdmApp, boolean deleteAll,
 201                         MapWrapper<TaxonNameBase> nameMap, MapWrapper<ReferenceBase> referenceMap){
 202
 203                 Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>();
 204
 205                 String dbAttrName;
 206                 String cdmAttrName;
 207
 208                 logger.info("start makeNameRelationships ...");
 209
 210                 INameService nameService = cdmApp.getNameService();
 211                 boolean delete = deleteAll;
 212
 213                 try {
 214                         //get data from database
 215                         String strQuery =
 216                                         " SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id " +
 217                                         " FROM Name as FromName INNER JOIN " +
 218                         " RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
 219                         " Name AS ToName ON RelName.NameFk2 = ToName.NameId "+
 220                     " WHERE (1=1)";
 221                         ResultSet rs = source.getResultSet(strQuery) ;
 222
 223                         int i = 0;
 224                         //for each reference
 225                         while (rs.next()){
 226
 227                                 if ((i++ % modCount) == 0){ logger.info("RelName handled: " + (i-1));}
 228
 229                                 int relNameId = rs.getInt("RelNameId");
 230                                 int name1Id = rs.getInt("name1Id");
 231                                 int name2Id = rs.getInt("name2Id");
 232                                 int relRefFk = rs.getInt("refFk");
 233                                 int relQualifierFk = rs.getInt("relNameQualifierFk");
 234
 235                                 TaxonNameBase nameFrom = nameMap.get(name1Id);
 236                                 TaxonNameBase nameTo = nameMap.get(name2Id);
 237
 238                                 //TODO
 239                                 ReferenceBase citation = null;
 240                                 String microcitation = null;
 241
 242                                 if (nameFrom != null && nameTo != null){
 243                                         if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
 244                                                 //TODO references, mikroref, etc
 245                                                 nameTo.setBasionym(nameFrom);
 246                                         }else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
 247                                                 String rule = null;  //TODO
 248                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), rule) ;
 249                                                 //TODO reference
 250                                         }else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
 251                                                 String rule = null;  //TODO
 252                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), rule) ;
 253                                                 //TODO reference
 254                                         }else if (relQualifierFk == NAME_REL_IS_TYPE_OF){
 255                                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 256                                                 //TODO reference
 257                                         }else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
 258                                                 String rule = null;  //TODO
 259                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), rule) ;
 260                                                 //TODO reference
 261                                         }else {
 262                                                 //TODO
 263                                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 264                                         }
 265                                         nameStore.add(nameFrom);
 266
 267                                         //TODO
 268                                         //Reference
 269                                         //ID
 270                                         //etc.
 271                                 }else{
 272                                         //TODO
 273                                         if (nameFrom == null){
 274                                                  logger.warn("from TaxonName for RelName (" + relNameId + ") does not exist in store");
 275                                         }
 276                                         if (nameTo == null){
 277                                                 logger.warn("to TaxonNames for RelName (" + relNameId + ") does not exist in store");
 278                                         }
 279                                 }
 280                         }
 281                         logger.info("TaxonName to save: " + nameStore.size());
 282                         nameService.saveTaxonNameAll(nameStore);
 283
 284                         logger.info("end makeRelName ...");
 285                         return true;
 286                 } catch (SQLException e) {
 287                         logger.error("SQLException:" +  e);
 288                         return false;
 289                 }
 290
 291         }
 292
 293 }