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

   1 package eu.etaxonomy.cdm.io.berlinModel;
   2
   3 import java.sql.ResultSet;
   4 import java.sql.SQLException;
   5 import java.util.HashMap;
   6 import java.util.List;
   7 import java.util.Map;
   8 import java.util.UUID;
   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.name.BotanicalName;
  17 import eu.etaxonomy.cdm.model.name.Rank;
  18 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  19 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  20 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  21 import eu.etaxonomy.cdm.strategy.exceptions.UnknownRankException;
  22
  23 public class BerlinModelTaxonNameIO {
  24         private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameIO.class);
  25
  26         private static int modCount = 1000;
  27
  28         public static boolean invoke(
  29                         Source source,
  30                         CdmApplicationController cdmApp,
  31                         boolean deleteAll,
  32                         MapWrapper<TaxonNameBase> taxonNameMap,
  33                         MapWrapper<ReferenceBase> referenceMap){
  34
  35
  36                 String dbAttrName;
  37                 String cdmAttrName;
  38                 boolean success = true ;
  39
  40                 logger.info("start makeTaxonNames ...");
  41                 INameService nameService = cdmApp.getNameService();
  42                 IReferenceService referenceService = cdmApp.getReferenceService();
  43                 boolean delete = deleteAll;
  44
  45
  46 //              if (delete){
  47 //                      List<TaxonNameBase> listAllNames =  nameService.getAllNames(0, 1000);
  48 //                      while(listAllNames.size() > 0 ){
  49 //                              for (TaxonNameBase name : listAllNames ){
  50 //                                      //FIXME
  51 //                                      //nameService.remove(name);
  52 //                              }
  53 //                              listAllNames =  nameService.getAllNames(0, 1000);
  54 //                      }
  55 //              }
  56
  57                 try {
  58
  59
  60                         //get data from database
  61                         String strQuery =
  62                                         "SELECT Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +
  63                                 " RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +
  64                                 " RefDetail.SecondarySources, RefDetail.IdInSource " +
  65                     " FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND Name.NomRefDetailFk = RefDetail.RefDetailId AND " +
  66                     " Name.NomRefFk = RefDetail.RefFk AND Name.NomRefFk = RefDetail.RefFk";
  67                         ResultSet rs = source.getResultSet(strQuery) ;
  68
  69                         int i = 0;
  70                         //for each reference
  71                         while (rs.next()){
  72
  73                                 if ((i++ % modCount) == 0){ logger.info("Names handled: " + (i-1));}
  74
  75                                 //create TaxonName element
  76                                 int nameId = rs.getInt("nameId");
  77                                 int rankId = rs.getInt("rankFk");
  78                                 Object nomRefFk = rs.getInt("NomRefFk");
  79
  80                                 try {
  81                                         logger.info(rankId);
  82                                         Rank rank = BerlinModelTransformer.rankId2Rank(rankId);
  83                                         //FIXME
  84                                         //BotanicalName name = BotanicalName.NewInstance(BerlinModelTransformer.rankId2Rank(rankId));
  85                                         BotanicalName botanicalName = new BotanicalName(rank);
  86
  87                                         if (rankId < 40){
  88                                                 dbAttrName = "supraGenericName";
  89                                         }else{
  90                                                 dbAttrName = "genus";
  91                                         }
  92                                         cdmAttrName = "genusOrUninomial";
  93                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  94
  95                                         dbAttrName = "genusSubdivisionEpi";
  96                                         cdmAttrName = "infraGenericEpithet";
  97                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  98
  99                                         dbAttrName = "speciesEpi";
 100                                         cdmAttrName = "specificEpithet";
 101                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 102
 103
 104                                         dbAttrName = "infraSpeciesEpi";
 105                                         cdmAttrName = "infraSpecificEpithet";
 106                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 107
 108                                         dbAttrName = "unnamedNamePhrase";
 109                                         cdmAttrName = "appendedPhrase";
 110                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 111
 112                                         dbAttrName = "preliminaryFlag";
 113                                         cdmAttrName = "XX" + "protectedTitleCache";
 114                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 115
 116                                         dbAttrName = "HybridFormulaFlag";
 117                                         cdmAttrName = "isHybridFormula";
 118                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 119
 120                                         dbAttrName = "MonomHybFlag";
 121                                         cdmAttrName = "isMonomHybrid";
 122                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 123
 124                                         dbAttrName = "BinomHybFlag";
 125                                         cdmAttrName = "isBinomHybrid";
 126                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 127
 128                                         dbAttrName = "TrinomHybFlag";
 129                                         cdmAttrName = "isTrinomHybrid";
 130                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 131
 132                                         //botanicalName.s
 133
 134 //                                      dbAttrName = "notes";
 135 //                                      cdmAttrName = "isTrinomHybrid";
 136 //                                      ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 137
 138                                         //TODO
 139                                         //Created
 140                                         //Note
 141                                         //makeAuthorTeams
 142                                         //CultivarGroupName
 143                                         //CultivarName
 144                                         //Source_Acc
 145                                         //OrthoProjection
 146
 147                                         //Details
 148
 149                                         dbAttrName = "details";
 150                                         cdmAttrName = "nomenclaturalMicroReference";
 151                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 152
 153                                         //TODO
 154                                         //preliminaryFlag
 155
 156                                         if (referenceMap != null){
 157                                                 if (nomRefFk != null){
 158                                                         int nomRefFkInt = (Integer)nomRefFk;
 159                                                         ReferenceBase nomenclaturalReference = referenceMap.get(nomRefFkInt);
 160                                                         if (INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
 161                                                                 botanicalName.setNomenclaturalReference((INomenclaturalReference)nomenclaturalReference);
 162                                                         }else{
 163                                                                 logger.error("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
 164                                                                                 " is not assignable from INomenclaturalReference. Relation was not set!!");
 165                                                         }
 166                                                 }
 167                                         }
 168
 169
 170                                         //name ID
 171                                         //refId
 172                                         //TODO
 173                                         // Annotation annotation = new Annotation("Berlin Model nameId: " + String.valueOf(refId), Language.DEFAULT());
 174                                         // botanicalName.addAnnotations(annotation);
 175
 176                                         taxonNameMap.put(nameId, botanicalName);
 177
 178                                 } catch (UnknownRankException e) {
 179                                         logger.warn("Name with id " + nameId + " has unknown rankId " + rankId + " and could not be saved.");
 180                                         success = false;
 181                                 }
 182
 183                         } //while rs.hasNext()
 184                         nameService.saveTaxonNameAll(taxonNameMap.objects());
 185
 186
 187 //                              //Code
 188 //                              strAttrName = "nomenclaturalCode";
 189 //                              strValue = "Botanical";
 190 //                              parent = elTaxonName;
 191 //                              xml.addStringAttribute(strValue, parent,  strAttrName, NS_NULL);
 192 //
 193 //                              //Simple
 194 //                              strDbAttr = "FullNameCache";
 195 //                              strElName = "Simple";
 196 //                              parent = elTaxonName;
 197 //                              xml.addElement(rs,strDbAttr, parent, strElName, nsTcs, OBLIGATORY);
 198 //
 199 //                              if (fullVersion){
 200 //                                      //Rank
 201 //                                      strDbAttr = "RankAbbrev";
 202 //                                      strElName = "Rank";
 203 //                                      parent = elTaxonName;
 204 //                                      xml.addElement(rs,strDbAttr, parent, strElName, nsTcs, OBLIGATORY);
 205 //
 206 //                                      //CanonicalName
 207 //                                      parent = elTaxonName;
 208 //                                      makeCanonicalName(rs, parent);
 209 //
 210 //
 211 //                                      //CanonicalAuthorship
 212 //                                      parent = elTaxonName;
 213 //                                      makeCanonicalAuthorship(rs, parent);
 214 //
 215 //                              }  //fi fullVersion
 216 //
 217 //                              //PublishedIn
 218 //                              strDbAttr = "NomRefFk";
 219 //                              strAttrName = "ref";
 220 //                              strElName = "PublishedIn";
 221 //                              parent = elTaxonName;
 222 //                              Attribute attrPublRef = xml.addAttributeInElement(rs, strDbAttr, parent, strAttrName, strElName, nsTcs, FACULTATIVE);
 223 //
 224 //                              if (attrPublRef != null){
 225 //                                      //does Publication exist?
 226 //                                      String ref = attrPublRef.getValue();
 227 //                                      if (! publicationMap.containsKey(ref)){
 228 //                                              logger.error("PublishedIn ref " + ref + " for " + nameId + " does not exist.");
 229 //                                      }
 230 //                              }
 231 //
 232 //
 233 //                              if (fullVersion){
 234 //                                      //Year
 235 //                                      String year = rs.getString("RefYear");
 236 //                                      if (year == null) {
 237 //                                              year = rs.getString("HigherRefYear");
 238 //                                      }
 239 //                                      strValue = year;
 240 //                                      strElName = "Year";
 241 //                                      parent = elTaxonName;
 242 //                                      xml.addStringElement(strValue, parent, strElName, nsTcs, FACULTATIVE);
 243 //
 244 //                                      //MicroReference
 245 //                                      strDbAttr = "Details";
 246 //                                      strElName = "MicroReference";
 247 //                                      parent = elTaxonName;
 248 //                                      xml.addElement(rs,strDbAttr, parent, strElName, nsTcs, FACULTATIVE);
 249 //
 250 //                              }//fi fullversion
 251 //                      }//while
 252 //
 253 //                      //insert related Names (Basionyms, ReplacedSyns, etc.
 254 //                      makeSpellingCorrections(nameMap);
 255 //                      makeBasionyms(nameMap);
 256 //                      makeLaterHomonyms(nameMap);
 257 //                      makeReplacedNames(nameMap);
 258 //
 259 //                      //insert Status infos
 260 //                      makeNameSpecificData(nameMap);
 261                         //cdmApp.flush();
 262                         logger.info("end makeTaxonNames ...");
 263                         return success;
 264                 } catch (SQLException e) {
 265                         logger.error("SQLException:" +  e);
 266                         return false;
 267                 }
 268
 269         }
 270
 271 }