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.List;
   6 import java.util.Map;
   7 import java.util.UUID;
   8
   9 import org.apache.log4j.Logger;
  10
  11 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  12 import eu.etaxonomy.cdm.api.service.INameService;
  13 import eu.etaxonomy.cdm.api.service.IReferenceService;
  14 import eu.etaxonomy.cdm.io.source.Source;
  15 import eu.etaxonomy.cdm.model.name.BotanicalName;
  16 import eu.etaxonomy.cdm.model.name.Rank;
  17 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  18 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  19 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  20 import eu.etaxonomy.cdm.strategy.exceptions.UnknownRankException;
  21
  22 public class BerlinModelTaxonNameIO {
  23         private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameIO.class);
  24
  25         private static int modCount = 1000;
  26
  27         public static boolean invoke(
  28                         Source source,
  29                         CdmApplicationController cdmApp,
  30                         boolean deleteAll,
  31                         Map<Integer, UUID> taxonNameMap,
  32                         Map<Integer, UUID> referenceMap){
  33
  34
  35                 String dbAttrName;
  36                 String cdmAttrName;
  37                 boolean success = true ;
  38
  39                 logger.info("start makeTaxonNames ...");
  40                 INameService nameService = cdmApp.getNameService();
  41                 IReferenceService referenceService = cdmApp.getReferenceService();
  42                 boolean delete = deleteAll;
  43
  44                 if (delete){
  45                         List<TaxonNameBase> listAllNames =  nameService.getAllNames(0, 1000);
  46                         while(listAllNames.size() > 0 ){
  47                                 for (TaxonNameBase name : listAllNames ){
  48                                         //FIXME
  49                                         //nameService.remove(name);
  50                                 }
  51                                 listAllNames =  nameService.getAllNames(0, 1000);
  52                         }
  53                 }
  54
  55                 try {
  56
  57
  58                         //get data from database
  59                         String strQuery =
  60                                         "SELECT TOP 102   Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +
  61                                 " RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +
  62                                 " RefDetail.SecondarySources, RefDetail.IdInSource " +
  63                     " FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND Name.NomRefDetailFk = RefDetail.RefDetailId AND " +
  64                     " Name.NomRefFk = RefDetail.RefFk AND Name.NomRefFk = RefDetail.RefFk";
  65                         ResultSet rs = source.getResultSet(strQuery) ;
  66
  67                         int i = 0;
  68                         //for each reference
  69                         while (rs.next()){
  70
  71                                 if ((i++ % modCount) == 0){ logger.info("Names handled: " + (i-1));}
  72
  73                                 //create TaxonName element
  74                                 int nameId = rs.getInt("nameId");
  75                                 int rankId = rs.getInt("rankFk");
  76                                 Object nomRefFk = rs.getInt("NomRefFk");
  77
  78                                 try {
  79                                         logger.info(rankId);
  80                                         Rank rank = BerlinModelTransformer.rankId2Rank(rankId);
  81                                         //FIXME
  82                                         //BotanicalName name = BotanicalName.NewInstance(BerlinModelTransformer.rankId2Rank(rankId));
  83                                         BotanicalName botanicalName = new BotanicalName(rank);
  84
  85                                         if (rankId < 40){
  86                                                 dbAttrName = "supraGenericName";
  87                                         }else{
  88                                                 dbAttrName = "genus";
  89                                         }
  90                                         cdmAttrName = "genusOrUninomial";
  91                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  92
  93                                         dbAttrName = "genusSubdivisionEpi";
  94                                         cdmAttrName = "infraGenericEpithet";
  95                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
  96
  97                                         dbAttrName = "speciesEpi";
  98                                         cdmAttrName = "specificEpithet";
  99                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 100
 101
 102                                         dbAttrName = "infraSpeciesEpi";
 103                                         cdmAttrName = "infraSpecificEpithet";
 104                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 105
 106                                         dbAttrName = "unnamedNamePhrase";
 107                                         cdmAttrName = "appendedPhrase";
 108                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 109
 110                                         dbAttrName = "preliminaryFlag";
 111                                         cdmAttrName = "XX" + "protectedTitleCache";
 112                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 113
 114                                         dbAttrName = "HybridFormulaFlag";
 115                                         cdmAttrName = "isHybridFormula";
 116                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 117
 118                                         dbAttrName = "MonomHybFlag";
 119                                         cdmAttrName = "isMonomHybrid";
 120                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 121
 122                                         dbAttrName = "BinomHybFlag";
 123                                         cdmAttrName = "isBinomHybrid";
 124                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 125
 126                                         dbAttrName = "TrinomHybFlag";
 127                                         cdmAttrName = "isTrinomHybrid";
 128                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 129
 130                                         //botanicalName.s
 131
 132 //                                      dbAttrName = "notes";
 133 //                                      cdmAttrName = "isTrinomHybrid";
 134 //                                      ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 135
 136                                         //TODO
 137                                         //Created
 138                                         //Note
 139                                         //makeAuthorTeams
 140                                         //CultivarGroupName
 141                                         //CultivarName
 142                                         //Source_Acc
 143                                         //OrthoProjection
 144
 145                                         //Details
 146
 147                                         dbAttrName = "details";
 148                                         cdmAttrName = "nomenclaturalMicroReference";
 149                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 150
 151                                         //TODO
 152                                         //preliminaryFlag
 153
 154                                         if (referenceMap != null){
 155                                                 if (nomRefFk != null){
 156                                                         int nomRefFkInt = (Integer)nomRefFk;
 157                                                         UUID referenceUuid = referenceMap.get(nomRefFkInt);
 158                                                         ReferenceBase nomenclaturalReference = referenceService.getReferenceByUuid(referenceUuid);
 159                                                         if (INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
 160                                                                 botanicalName.setNomenclaturalReference((INomenclaturalReference)nomenclaturalReference);
 161                                                         }else{
 162                                                                 logger.error("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
 163                                                                                 " is not assignable from INomenclaturalReference. Relation was not set!!");
 164                                                         }
 165                                                 }
 166                                         }
 167
 168
 169                                         //name ID
 170                                         //refId
 171                                         //TODO
 172                                         // Annotation annotation = new Annotation("Berlin Model nameId: " + String.valueOf(refId), Language.DEFAULT());
 173                                         // botanicalName.addAnnotations(annotation);
 174
 175
 176                                         UUID nameUuid = nameService.saveTaxonName(botanicalName);
 177                                         taxonNameMap.put(nameId, nameUuid);
 178
 179                                 } catch (UnknownRankException e) {
 180                                         logger.warn("Name with id " + nameId + " has unknown rankId " + rankId + " and could not be saved.");
 181                                         success = false;
 182                                 }
 183
 184                         }
 185
 186 //                              //Code
 187 //                              strAttrName = "nomenclaturalCode";
 188 //                              strValue = "Botanical";
 189 //                              parent = elTaxonName;
 190 //                              xml.addStringAttribute(strValue, parent,  strAttrName, NS_NULL);
 191 //
 192 //                              //Simple
 193 //                              strDbAttr = "FullNameCache";
 194 //                              strElName = "Simple";
 195 //                              parent = elTaxonName;
 196 //                              xml.addElement(rs,strDbAttr, parent, strElName, nsTcs, OBLIGATORY);
 197 //
 198 //                              if (fullVersion){
 199 //                                      //Rank
 200 //                                      strDbAttr = "RankAbbrev";
 201 //                                      strElName = "Rank";
 202 //                                      parent = elTaxonName;
 203 //                                      xml.addElement(rs,strDbAttr, parent, strElName, nsTcs, OBLIGATORY);
 204 //
 205 //                                      //CanonicalName
 206 //                                      parent = elTaxonName;
 207 //                                      makeCanonicalName(rs, parent);
 208 //
 209 //
 210 //                                      //CanonicalAuthorship
 211 //                                      parent = elTaxonName;
 212 //                                      makeCanonicalAuthorship(rs, parent);
 213 //
 214 //                              }  //fi fullVersion
 215 //
 216 //                              //PublishedIn
 217 //                              strDbAttr = "NomRefFk";
 218 //                              strAttrName = "ref";
 219 //                              strElName = "PublishedIn";
 220 //                              parent = elTaxonName;
 221 //                              Attribute attrPublRef = xml.addAttributeInElement(rs, strDbAttr, parent, strAttrName, strElName, nsTcs, FACULTATIVE);
 222 //
 223 //                              if (attrPublRef != null){
 224 //                                      //does Publication exist?
 225 //                                      String ref = attrPublRef.getValue();
 226 //                                      if (! publicationMap.containsKey(ref)){
 227 //                                              logger.error("PublishedIn ref " + ref + " for " + nameId + " does not exist.");
 228 //                                      }
 229 //                              }
 230 //
 231 //
 232 //                              if (fullVersion){
 233 //                                      //Year
 234 //                                      String year = rs.getString("RefYear");
 235 //                                      if (year == null) {
 236 //                                              year = rs.getString("HigherRefYear");
 237 //                                      }
 238 //                                      strValue = year;
 239 //                                      strElName = "Year";
 240 //                                      parent = elTaxonName;
 241 //                                      xml.addStringElement(strValue, parent, strElName, nsTcs, FACULTATIVE);
 242 //
 243 //                                      //MicroReference
 244 //                                      strDbAttr = "Details";
 245 //                                      strElName = "MicroReference";
 246 //                                      parent = elTaxonName;
 247 //                                      xml.addElement(rs,strDbAttr, parent, strElName, nsTcs, FACULTATIVE);
 248 //
 249 //                              }//fi fullversion
 250 //                      }//while
 251 //
 252 //                      //insert related Names (Basionyms, ReplacedSyns, etc.
 253 //                      makeSpellingCorrections(nameMap);
 254 //                      makeBasionyms(nameMap);
 255 //                      makeLaterHomonyms(nameMap);
 256 //                      makeReplacedNames(nameMap);
 257 //
 258 //                      //insert Status infos
 259 //                      makeNameSpecificData(nameMap);
 260                         //cdmApp.flush();
 261                         logger.info("end makeTaxonNames ...");
 262                         return success;
 263                 } catch (SQLException e) {
 264                         logger.error("SQLException:" +  e);
 265                         return false;
 266                 }
 267
 268         }
 269
 270 }