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.net.MalformedURLException;
   6 import java.net.URL;
   7 import java.sql.ResultSet;
   8 import java.sql.SQLException;
   9 import java.util.HashSet;
  10 import java.util.Set;
  11
  12 import org.apache.log4j.Logger;
  13
  14 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  15 import eu.etaxonomy.cdm.api.service.INameService;
  16 import eu.etaxonomy.cdm.api.service.IReferenceService;
  17 import eu.etaxonomy.cdm.io.source.Source;
  18 import eu.etaxonomy.cdm.model.agent.Agent;
  19 import eu.etaxonomy.cdm.model.agent.Person;
  20 import eu.etaxonomy.cdm.model.agent.Team;
  21 import eu.etaxonomy.cdm.model.common.Annotation;
  22 import eu.etaxonomy.cdm.model.common.Language;
  23 import eu.etaxonomy.cdm.model.common.Marker;
  24 import eu.etaxonomy.cdm.model.common.MarkerType;
  25 import eu.etaxonomy.cdm.model.name.BotanicalName;
  26 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  27 import eu.etaxonomy.cdm.model.name.Rank;
  28 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  29 import eu.etaxonomy.cdm.model.reference.INomenclaturalReference;
  30 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  31 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  32
  33
  34 public class BerlinModelTaxonNameIO {
  35         private static final Logger logger = Logger.getLogger(BerlinModelTaxonNameIO.class);
  36
  37         private static int modCount = 5000;
  38
  39         //TODO
  40         static boolean invokeStatus(ReferenceBase berlinModelRef, Source source, CdmApplicationController cdmApp,
  41                         boolean deleteAll, MapWrapper<TaxonNameBase> taxonNameMap,
  42                         MapWrapper<ReferenceBase> referenceMap, MapWrapper<Agent> authorMap){
  43                 return false;
  44         }
  45
  46         public static boolean invoke(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp,
  47                         MapWrapper<TaxonNameBase> taxonNameMap, MapWrapper<ReferenceBase> referenceMap, MapWrapper<Team> authorMap){
  48
  49                 Source source = bmiConfig.getSource();
  50                 String dbAttrName;
  51                 String cdmAttrName;
  52                 boolean success = true ;
  53
  54                 logger.info("start makeTaxonNames ...");
  55                 INameService nameService = cdmApp.getNameService();
  56                 boolean delete = bmiConfig.isDeleteAll();
  57
  58                 try {
  59
  60
  61                         //get data from database
  62                         String strQuery =
  63                                         "SELECT Name.* , RefDetail.RefDetailId, RefDetail.RefFk, " +
  64                                 " RefDetail.FullRefCache, RefDetail.FullNomRefCache, RefDetail.PreliminaryFlag AS RefDetailPrelim, RefDetail.Details, " +
  65                                 " RefDetail.SecondarySources, RefDetail.IdInSource " +
  66                     " FROM Name LEFT OUTER JOIN RefDetail ON Name.NomRefDetailFk = RefDetail.RefDetailId AND Name.NomRefDetailFk = RefDetail.RefDetailId AND " +
  67                         " Name.NomRefFk = RefDetail.RefFk AND Name.NomRefFk = RefDetail.RefFk" +
  68                     " WHERE (1=1) ";
  69                                         //strQuery += " AND Name.Created_When > '03.03.2004' ";
  70
  71
  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("Names handled: " + (i-1));}
  79
  80                                 //create TaxonName element
  81                                 int nameId = rs.getInt("nameId");
  82                                 int rankId = rs.getInt("rankFk");
  83                                 Object authorFk = rs.getObject("AuthorTeamFk");
  84                                 Object exAuthorFk = rs.getObject("ExAuthorTeamFk");
  85                                 Object basAuthorFk = rs.getObject("BasAuthorTeamFk");
  86                                 Object exBasAuthorFk = rs.getObject("ExBasAuthorTeamFk");
  87                                 Object nomRefFk = rs.getObject("NomRefFk");
  88
  89                                 Object createdWhen = rs.getObject("Created_When");
  90                                 Object createdWho = rs.getObject("Created_Who");
  91 //                              Object updatedWhen = rs.getObject("Updated_When");
  92 //                              Object updatedWho = rs.getObject("Updated_who");
  93                                 Object updatedWhen = "";
  94                                 Object updatedWho = "";
  95                                 Object notes = rs.getObject("notes");
  96
  97                                 try {
  98                                         if (logger.isDebugEnabled()){logger.debug(rankId);}
  99                                         Rank rank = BerlinModelTransformer.rankId2Rank(rankId);
 100                                         //FIXME
 101                                         //BotanicalName name = BotanicalName.NewInstance(BerlinModelTransformer.rankId2Rank(rankId));
 102                                         BotanicalName botanicalName = BotanicalName.NewInstance(rank);
 103
 104                                         if (rankId < 40){
 105                                                 dbAttrName = "supraGenericName";
 106                                         }else{
 107                                                 dbAttrName = "genus";
 108                                         }
 109                                         cdmAttrName = "genusOrUninomial";
 110                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 111
 112                                         dbAttrName = "genusSubdivisionEpi";
 113                                         cdmAttrName = "infraGenericEpithet";
 114                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 115
 116                                         dbAttrName = "speciesEpi";
 117                                         cdmAttrName = "specificEpithet";
 118                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 119
 120
 121                                         dbAttrName = "infraSpeciesEpi";
 122                                         cdmAttrName = "infraSpecificEpithet";
 123                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 124
 125                                         dbAttrName = "unnamedNamePhrase";
 126                                         cdmAttrName = "appendedPhrase";
 127                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 128
 129                                         dbAttrName = "preliminaryFlag";
 130                                         cdmAttrName = "XX" + "protectedTitleCache";
 131                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 132
 133                                         dbAttrName = "HybridFormulaFlag";
 134                                         cdmAttrName = "isHybridFormula";
 135                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 136
 137                                         dbAttrName = "MonomHybFlag";
 138                                         cdmAttrName = "isMonomHybrid";
 139                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 140
 141                                         dbAttrName = "BinomHybFlag";
 142                                         cdmAttrName = "isBinomHybrid";
 143                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 144
 145                                         dbAttrName = "TrinomHybFlag";
 146                                         cdmAttrName = "isTrinomHybrid";
 147                                         success &= ImportHelper.addBooleanValue(rs, botanicalName, dbAttrName, cdmAttrName);
 148
 149                                         //botanicalName.s
 150
 151 //                                      dbAttrName = "notes";
 152 //                                      cdmAttrName = "isTrinomHybrid";
 153 //                                      ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 154
 155                                         //TODO
 156                                         //Created
 157                                         //Note
 158                                         //makeAuthorTeams
 159                                         //CultivarGroupName
 160                                         //CultivarName
 161                                         //Source_Acc
 162                                         //OrthoProjection
 163
 164                                         //Details
 165
 166                                         dbAttrName = "details";
 167                                         cdmAttrName = "nomenclaturalMicroReference";
 168                                         success &= ImportHelper.addStringValue(rs, botanicalName, dbAttrName, cdmAttrName);
 169
 170                                         //TODO
 171                                         //preliminaryFlag
 172
 173                                         //authorTeams
 174                                         if (authorMap != null){
 175                                                 botanicalName.setCombinationAuthorTeam(getAuthorTeam(authorMap, authorFk, nameId));
 176                                                 botanicalName.setExCombinationAuthorTeam(getAuthorTeam(authorMap, exAuthorFk, nameId));
 177                                                 botanicalName.setBasionymAuthorTeam(getAuthorTeam(authorMap, basAuthorFk, nameId));
 178                                                 botanicalName.setExBasionymAuthorTeam(getAuthorTeam(authorMap, exBasAuthorFk, nameId));
 179                                         }
 180
 181                                         //nomenclatural Reference
 182                                         if (referenceMap != null){
 183                                                 if (nomRefFk != null){
 184                                                         int nomRefFkInt = (Integer)nomRefFk;
 185                                                         ReferenceBase nomenclaturalReference = referenceMap.get(nomRefFkInt);
 186                                                         if (nomenclaturalReference == null){
 187                                                                 //TODO
 188                                                                 logger.warn("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
 189                                                                 " was not found in reference store. Relation was not set!!");
 190                                                         }else if (! INomenclaturalReference.class.isAssignableFrom(nomenclaturalReference.getClass())){
 191                                                                 logger.error("Nomenclatural reference (nomRefFk = " + nomRefFkInt + ") for TaxonName (nameId = " + nameId + ")"+
 192                                                                 " is not assignable from INomenclaturalReference. Relation was not set!! (Class = " + nomenclaturalReference.getClass()+ ")");
 193                                                         }else{
 194                                                                 botanicalName.setNomenclaturalReference((INomenclaturalReference)nomenclaturalReference);
 195                                                         }
 196                                                 }
 197                                         }
 198
 199                                         //refId
 200                                         String createdAnnotationString = "Berlin Model record was created By: " + String.valueOf(createdWho) + " (" + String.valueOf(createdWhen) + ") " +
 201                                                                                         " and updated By: " + String.valueOf(updatedWho) + " (" + String.valueOf(updatedWhen) + ")";
 202                                         Annotation annotation = Annotation.NewInstance(createdAnnotationString, Language.ENGLISH());
 203                                         annotation.setCommentator(bmiConfig.getCommentator());
 204 //                                      try {
 205 //                                              URL linkbackUrl = new URL("http:\\www.abc.de");
 206 //                                              annotation.setLinkbackUrl(linkbackUrl);
 207 //                                      } catch (MalformedURLException e) {
 208 //                                              logger.warn("MalformedURLException");
 209 //                                      }
 210                                         botanicalName.addAnnotation(annotation);
 211
 212                                         if (notes != null){
 213                                                 String notesString = String.valueOf(notes);
 214                                                 if (notesString.length() > 254 ){
 215                                                         notesString = notesString.substring(0, 250) + "...";
 216                                                 }
 217                                                 Annotation notesAnnotation = Annotation.NewInstance(notesString, null);
 218                                                 //notes.setCommentator(bmiConfig.getCommentator());
 219                                                 botanicalName.addAnnotation(notesAnnotation);
 220                                         }
 221
 222
 223                                         boolean flag = true;
 224                                         Marker marker = Marker.NewInstance(MarkerType.TO_BE_CHECKED() ,flag);
 225                                         botanicalName.addMarker(marker);
 226
 227
 228                                         //nameId
 229                                         ImportHelper.setOriginalSource(botanicalName, bmiConfig.getSourceReference(), nameId);
 230
 231                                         taxonNameMap.put(nameId, botanicalName);
 232
 233                                 }
 234                                 catch (UnknownCdmTypeException e) {
 235                                         logger.warn("Name with id " + nameId + " has unknown rankId " + rankId + " and could not be saved.");
 236                                         success = false;
 237                                 }
 238
 239                         } //while rs.hasNext()
 240                         logger.info(i + " names handled");
 241                         nameService.saveTaxonNameAll(taxonNameMap.objects());
 242
 243 //                      makeNameSpecificData(nameMap);
 244
 245                         logger.info("end makeTaxonNames ...");
 246                         return success;
 247                 } catch (SQLException e) {
 248                         logger.error("SQLException:" +  e);
 249                         return false;
 250                 }
 251
 252         }
 253
 254         private static Team getAuthorTeam(MapWrapper<Team> authorMap, Object teamIdObject, int nameId){
 255                 if (teamIdObject == null){
 256                         return null;
 257                 }else {
 258                         int teamId = (Integer)teamIdObject;
 259                         Team team = authorMap.get(teamId);
 260                         if (team == null){
 261                                 //TODO
 262                                 logger.warn("AuthorTeam (teamId = " + teamId + ") for TaxonName (nameId = " + nameId + ")"+
 263                                 " was not found in authorTeam store. Relation was not set!!");
 264                                 return null;
 265                         }else{
 266                                 return team;
 267                         }
 268                 }
 269         }
 270
 271
 272         public static boolean invokeRelations(BerlinModelImportConfigurator bmiConfig, CdmApplicationController cdmApp,
 273                         MapWrapper<TaxonNameBase> nameMap, MapWrapper<ReferenceBase> referenceMap){
 274
 275                 Set<TaxonNameBase> nameStore = new HashSet<TaxonNameBase>();
 276                 Source source = bmiConfig.getSource();
 277                 String dbAttrName;
 278                 String cdmAttrName;
 279
 280                 logger.info("start makeNameRelationships ...");
 281
 282                 INameService nameService = cdmApp.getNameService();
 283                 boolean delete = bmiConfig.isDeleteAll();
 284
 285                 try {
 286                         //get data from database
 287                         String strQuery =
 288                                         " SELECT RelName.*, FromName.nameId as name1Id, ToName.nameId as name2Id " +
 289                                         " FROM Name as FromName INNER JOIN " +
 290                         " RelName ON FromName.NameId = RelName.NameFk1 INNER JOIN " +
 291                         " Name AS ToName ON RelName.NameFk2 = ToName.NameId "+
 292                     " WHERE (1=1)";
 293                         ResultSet rs = source.getResultSet(strQuery) ;
 294
 295                         int i = 0;
 296                         //for each reference
 297                         while (rs.next()){
 298
 299                                 if ((i++ % modCount) == 0){ logger.info("RelName handled: " + (i-1));}
 300
 301                                 int relNameId = rs.getInt("RelNameId");
 302                                 int name1Id = rs.getInt("name1Id");
 303                                 int name2Id = rs.getInt("name2Id");
 304                                 int relRefFk = rs.getInt("refFk");
 305                                 int relQualifierFk = rs.getInt("relNameQualifierFk");
 306
 307                                 TaxonNameBase nameFrom = nameMap.get(name1Id);
 308                                 TaxonNameBase nameTo = nameMap.get(name2Id);
 309
 310                                 //TODO
 311                                 ReferenceBase citation = null;
 312                                 String microcitation = null;
 313
 314                                 if (nameFrom != null && nameTo != null){
 315                                         if (relQualifierFk == NAME_REL_IS_BASIONYM_FOR){
 316                                                 //TODO references, mikroref, etc
 317                                                 nameTo.setBasionym(nameFrom);
 318                                         }else if (relQualifierFk == NAME_REL_IS_LATER_HOMONYM_OF){
 319                                                 String rule = null;  //TODO
 320                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.LATER_HOMONYM(), rule) ;
 321                                                 //TODO reference
 322                                         }else if (relQualifierFk == NAME_REL_IS_REPLACED_SYNONYM_FOR){
 323                                                 String rule = null;  //TODO
 324                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.REPLACED_SYNONYM(), rule) ;
 325                                                 //TODO reference
 326                                         }else if (relQualifierFk == NAME_REL_IS_TYPE_OF){
 327                                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 328                                                 //TODO reference
 329                                         }else if (relQualifierFk == NAME_REL_IS_ORTHOGRAPHIC_VARIANT_OF){
 330                                                 String rule = null;  //TODO
 331                                                 nameFrom.addRelationshipToName(nameTo, NameRelationshipType.ORTHOGRAPHIC_VARIANT(), rule) ;
 332                                                 //TODO reference
 333                                         }else {
 334                                                 //TODO
 335                                                 logger.warn("NameRelationShipType " + relQualifierFk + " not yet implemented");
 336                                         }
 337                                         nameStore.add(nameFrom);
 338
 339                                         //TODO
 340                                         //Reference
 341                                         //ID
 342                                         //etc.
 343                                 }else{
 344                                         //TODO
 345                                         if (nameFrom == null){
 346                                                  logger.warn("from TaxonName for RelName (" + relNameId + ") does not exist in store");
 347                                         }
 348                                         if (nameTo == null){
 349                                                 logger.warn("to TaxonNames for RelName (" + relNameId + ") does not exist in store");
 350                                         }
 351                                 }
 352                         }
 353                         logger.info("TaxonName to save: " + nameStore.size());
 354                         nameService.saveTaxonNameAll(nameStore);
 355
 356                         logger.info("end makeRelName ...");
 357                         return true;
 358                 } catch (SQLException e) {
 359                         logger.error("SQLException:" +  e);
 360                         return false;
 361                 }
 362
 363         }
 364
 365 }