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

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.io.berlinModel;
  11
  12 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_ACCEPTED;
  13 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_PARTIAL_SYN;
  14 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_PRO_PARTE_SYN;
  15 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.T_STATUS_SYNONYM;
  16
  17 import java.sql.ResultSet;
  18 import java.sql.SQLException;
  19 import java.util.Map;
  20 import java.util.UUID;
  21
  22 import org.apache.log4j.Logger;
  23 import org.springframework.stereotype.Component;
  24
  25 import eu.etaxonomy.cdm.io.common.ICdmIO;
  26 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  27 import eu.etaxonomy.cdm.io.common.ImportHelper;
  28 import eu.etaxonomy.cdm.io.common.MapWrapper;
  29 import eu.etaxonomy.cdm.io.common.Source;
  30 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  31 import eu.etaxonomy.cdm.model.common.CdmBase;
  32 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  33 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  34 import eu.etaxonomy.cdm.model.taxon.Synonym;
  35 import eu.etaxonomy.cdm.model.taxon.Taxon;
  36 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  37
  38
  39 /**
  40  * @author a.mueller
  41  * @created 20.03.2008
  42  * @version 1.0
  43  */
  44 @Component
  45 public class BerlinModelTaxonImport  extends BerlinModelImportBase  {
  46         private static final Logger logger = Logger.getLogger(BerlinModelTaxonImport.class);
  47
  48         private int modCount = 10000;
  49
  50         public BerlinModelTaxonImport(){
  51                 super();
  52         }
  53
  54         /* (non-Javadoc)
  55          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  56          */
  57         @Override
  58         protected boolean doCheck(IImportConfigurator config){
  59                 boolean result = true;
  60                 BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
  61                 logger.warn("Checking for Taxa not yet fully implemented");
  62                 result &= checkTaxonStatus(bmiConfig);
  63                 result &= checkInactivated(bmiConfig);
  64
  65                 return result;
  66         }
  67
  68         private boolean checkTaxonStatus(BerlinModelImportConfigurator bmiConfig){
  69                 try {
  70                         boolean result = true;
  71                         Source source = bmiConfig.getSource();
  72                         String strSQL = " SELECT RelPTaxon.RelQualifierFk, RelPTaxon.relPTaxonId, PTaxon.PTNameFk, PTaxon.PTRefFk, PTaxon_1.PTNameFk AS Expr1, PTaxon.RIdentifier, PTaxon_1.RIdentifier AS Expr3, Name.FullNameCache "  +
  73                                 " FROM RelPTaxon " +
  74                                         " INNER JOIN PTaxon ON RelPTaxon.PTNameFk1 = PTaxon.PTNameFk AND RelPTaxon.PTRefFk1 = PTaxon.PTRefFk " +
  75                                         " INNER JOIN PTaxon AS PTaxon_1 ON RelPTaxon.PTNameFk2 = PTaxon_1.PTNameFk AND RelPTaxon.PTRefFk2 = PTaxon_1.PTRefFk  " +
  76                                         " INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
  77                                 " WHERE (dbo.PTaxon.StatusFk = 1) AND ((RelPTaxon.RelQualifierFk = 7) OR (RelPTaxon.RelQualifierFk = 6) OR (RelPTaxon.RelQualifierFk = 2)) ";
  78                         ResultSet rs = source.getResultSet(strSQL);
  79                         boolean firstRow = true;
  80                         int i = 0;
  81                         while (rs.next()){
  82                                 i++;
  83                                 if (firstRow){
  84                                         System.out.println("========================================================");
  85                                         logger.warn("There are taxa that have a 'is synonym of' - relationship but having taxon status 'accepted'!");
  86                                         System.out.println("========================================================");
  87                                 }
  88                                 int rIdentifier = rs.getInt("RIdentifier");
  89                                 int nameFk = rs.getInt("PTNameFk");
  90                                 int refFk = rs.getInt("PTRefFk");
  91                                 int relPTaxonId = rs.getInt("relPTaxonId");
  92                                 String taxonName = rs.getString("FullNameCache");
  93
  94                                 System.out.println("RIdentifier:" + rIdentifier + "\n  name: " + nameFk +
  95                                                 "\n  taxonName: " + taxonName + "\n  refId: " + refFk + "\n  RelPTaxonId: " + relPTaxonId );
  96                                 result = firstRow = false;
  97                         }
  98                         if (i > 0){
  99                                 System.out.println(" ");
 100                         }
 101
 102                         return result;
 103                 } catch (SQLException e) {
 104                         e.printStackTrace();
 105                         return false;
 106                 }
 107         }
 108
 109         private boolean checkInactivated(BerlinModelImportConfigurator bmiConfig){
 110                 try {
 111                         boolean result = true;
 112                         Source source = bmiConfig.getSource();
 113                         String strSQL = " SELECT * "  +
 114                                 " FROM PTaxon " +
 115                                         " INNER JOIN Name ON PTaxon.PTNameFk = Name.NameId " +
 116                                 " WHERE (PTaxon.DoubtfulFlag = 'i') ";
 117                         ResultSet rs = source.getResultSet(strSQL);
 118                         boolean firstRow = true;
 119                         int i = 0;
 120                         while (rs.next()){
 121                                 i++;
 122                                 if (firstRow){
 123                                         System.out.println("========================================================");
 124                                         logger.warn("There are taxa that have a doubtful flag 'i'(inactivated). Inactivated is not supported by CDM!");
 125                                         System.out.println("========================================================");
 126                                 }
 127                                 int rIdentifier = rs.getInt("RIdentifier");
 128                                 int nameFk = rs.getInt("PTNameFk");
 129                                 int refFk = rs.getInt("PTRefFk");
 130                                 String taxonName = rs.getString("FullNameCache");
 131
 132                                 System.out.println("RIdentifier:" + rIdentifier + "\n  nameId: " + nameFk +
 133                                                 "\n  taxonName: " + taxonName + "\n  refId: " + refFk  );
 134                                 result = firstRow = false;
 135                         }
 136                         if (i > 0){
 137                                 System.out.println(" ");
 138                         }
 139
 140                         return result;
 141                 } catch (SQLException e) {
 142                         e.printStackTrace();
 143                         return false;
 144                 }
 145         }
 146
 147         /* (non-Javadoc)
 148          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
 149          */
 150         @Override
 151         protected boolean doInvoke(IImportConfigurator config,
 152                         Map<String, MapWrapper<? extends CdmBase>> stores){
 153
 154                 //make not needed maps empty
 155                 String teamStore = ICdmIO.TEAM_STORE;
 156                 MapWrapper<? extends CdmBase> store = stores.get(teamStore);
 157                 MapWrapper<TeamOrPersonBase> teamMap = (MapWrapper<TeamOrPersonBase>)store;
 158                 teamMap.makeEmpty();
 159
 160
 161                 MapWrapper<TaxonNameBase<?,?>> taxonNameMap = (MapWrapper<TaxonNameBase<?,?>>)stores.get(ICdmIO.TAXONNAME_STORE);
 162                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.REFERENCE_STORE);
 163                 MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)stores.get(ICdmIO.NOMREF_STORE);
 164                 MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
 165
 166                 BerlinModelImportConfigurator bmiConfig = (BerlinModelImportConfigurator)config;
 167                 Source source = bmiConfig.getSource();
 168
 169                 logger.info("start makeTaxa ...");
 170
 171                 String namespace = "PTaxon";
 172
 173                 try {
 174                         //get data from database
 175                         String strQuery =
 176                                         " SELECT * " +
 177                                         " FROM PTaxon " +
 178                                         " WHERE (1=1)";
 179
 180                         ResultSet rs = source.getResultSet(strQuery) ;
 181
 182                         int i = 0;
 183                         //for each reference
 184                         while (rs.next()){
 185
 186                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("PTaxa handled: " + (i-1));}
 187
 188                                 //create TaxonName element
 189                                 int taxonId = rs.getInt("RIdentifier");
 190                                 int statusFk = rs.getInt("statusFk");
 191
 192                                 int nameFk = rs.getInt("PTNameFk");
 193                                 int refFk = rs.getInt("PTRefFk");
 194                                 String doubtful = rs.getString("DoubtfulFlag");
 195                                 String uuid = null;
 196                                 if (resultSetHasColumn(rs,"UUID")){
 197                                         uuid = rs.getString("UUID");
 198                                 }
 199
 200                                 TaxonNameBase<?,?> taxonName = null;
 201                                 if (taxonNameMap != null){
 202                                         taxonName  = taxonNameMap.get(nameFk);
 203                                 }
 204
 205                                 ReferenceBase reference = null;
 206                                 if (referenceMap != null){
 207                                         reference = referenceMap.get(refFk);
 208                                         if (reference == null){
 209                                                 reference = nomRefMap.get(refFk);
 210                                         }
 211                                 }
 212
 213                                 if(! config.isIgnoreNull()){
 214                                         if (taxonName == null ){
 215                                                 logger.warn("TaxonName belonging to taxon (RIdentifier = " + taxonId + ") could not be found in store. Taxon will not be transported");
 216                                                 continue; //next taxon
 217                                         }else if (reference == null ){
 218                                                 logger.warn("Reference belonging to taxon could not be found in store. Taxon will not be imported");
 219                                                 continue; //next taxon
 220                                         }
 221                                 }
 222                                 TaxonBase taxonBase;
 223                                 Synonym synonym;
 224                                 Taxon taxon;
 225                                 try {
 226                                         logger.debug(statusFk);
 227                                         if (statusFk == T_STATUS_ACCEPTED){
 228                                                 taxon = Taxon.NewInstance(taxonName, reference);
 229                                                 taxonBase = taxon;
 230                                         }else if (statusFk == T_STATUS_SYNONYM || statusFk == T_STATUS_PRO_PARTE_SYN || statusFk == T_STATUS_PARTIAL_SYN){
 231                                                 synonym = Synonym.NewInstance(taxonName, reference);
 232                                                 taxonBase = synonym;
 233                                                 if (statusFk == T_STATUS_PRO_PARTE_SYN){
 234                                                         bmiConfig.addProParteSynonym(synonym);
 235                                                 }
 236                                                 if (statusFk == T_STATUS_PARTIAL_SYN){
 237                                                         bmiConfig.addPartialSynonym(synonym);
 238                                                 }
 239                                         }else{
 240                                                 logger.warn("TaxonStatus " + statusFk + " not yet implemented. Taxon (RIdentifier = " + taxonId + ") left out.");
 241                                                 continue;
 242                                         }
 243                                         if (uuid != null){
 244                                                 taxonBase.setUuid(UUID.fromString(uuid));
 245                                         }
 246
 247                                         //TODO
 248 //                                              dbAttrName = "Detail";
 249 //                                              cdmAttrName = "Micro";
 250 //                                              ImportHelper.addStringValue(rs, taxonBase, dbAttrName, cdmAttrName);
 251
 252                                         if (doubtful.equals("a")){
 253                                                 taxonBase.setDoubtful(false);
 254                                         }else if(doubtful.equals("d")){
 255                                                 taxonBase.setDoubtful(true);
 256                                         }else if(doubtful.equals("i")){
 257                                                 //TODO
 258                                                 logger.warn("Doubtful = i (inactivated) not yet implemented. Doubtful set to false");
 259                                         }
 260
 261                                         //nameId
 262                                         ImportHelper.setOriginalSource(taxonBase, bmiConfig.getSourceReference(), taxonId, namespace);
 263
 264
 265                                         //TODO
 266                                         //
 267                                         //Created
 268                                         //Note
 269                                         //ALL
 270
 271                                         taxonMap.put(taxonId, taxonBase);
 272                                 } catch (Exception e) {
 273                                         logger.warn("An exception occurred when creating taxon with id " + taxonId + ". Taxon could not be saved.");
 274                                 }
 275                         }
 276                         //invokeRelations(source, cdmApp, deleteAll, taxonMap, referenceMap);
 277                         logger.info("saving taxa ...");
 278                         getTaxonService().saveTaxonAll(taxonMap.objects());
 279
 280                         logger.info("end makeTaxa ...");
 281
 282                         return true;
 283                 } catch (SQLException e) {
 284                         logger.error("SQLException:" +  e);
 285                         return false;
 286                 }
 287
 288         }
 289
 290
 291
 292         /* (non-Javadoc)
 293          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 294          */
 295         protected boolean isIgnore(IImportConfigurator config){
 296                 return ! config.isDoTaxa();
 297         }
 298
 299 }