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

   1 package eu.etaxonomy.cdm.io.berlinModel;
   2
   3 import static eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer.*;
   4 import java.sql.ResultSet;
   5 import java.sql.SQLException;
   6 import java.util.ArrayList;
   7 import java.util.Collection;
   8 import java.util.HashMap;
   9 import java.util.Iterator;
  10 import java.util.List;
  11 import java.util.Map;
  12 import java.util.UUID;
  13
  14 import org.apache.log4j.Logger;
  15 import org.springframework.stereotype.Service;
  16
  17 import eu.etaxonomy.cdm.api.application.CdmApplicationController;
  18 import eu.etaxonomy.cdm.api.service.IAgentService;
  19 import eu.etaxonomy.cdm.api.service.INameService;
  20 import eu.etaxonomy.cdm.api.service.IReferenceService;
  21 import eu.etaxonomy.cdm.api.service.IService;
  22 import eu.etaxonomy.cdm.api.service.ITaxonService;
  23 import eu.etaxonomy.cdm.io.source.Source;
  24 import eu.etaxonomy.cdm.model.agent.Agent;
  25 import eu.etaxonomy.cdm.model.name.BotanicalName;
  26 import eu.etaxonomy.cdm.model.name.Rank;
  27 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  28 import eu.etaxonomy.cdm.model.reference.Article;
  29 import eu.etaxonomy.cdm.model.reference.Book;
  30 import eu.etaxonomy.cdm.model.reference.BookSection;
  31 import eu.etaxonomy.cdm.model.reference.Database;
  32 import eu.etaxonomy.cdm.model.reference.Generic;
  33 import eu.etaxonomy.cdm.model.reference.Journal;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  35 import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
  36 import eu.etaxonomy.cdm.model.taxon.Synonym;
  37 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  38 import eu.etaxonomy.cdm.model.taxon.Taxon;
  39 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  40 import eu.etaxonomy.cdm.strategy.exceptions.UnknownRankException;
  41
  42 @Service
  43 public class BerlinModelImport {
  44         private static final Logger logger = Logger.getLogger(BerlinModelImport.class);
  45
  46         private boolean deleteAll = false;
  47
  48         //BerlinModelDB
  49         private Source source;
  50
  51         //CdmApplication
  52         private CdmApplicationController cdmApp;
  53
  54         //Constants
  55         //final boolean OBLIGATORY = true;
  56         //final boolean FACULTATIVE = false;
  57         final int modCount = 1000;
  58
  59
  60         //Hashmaps for Joins
  61         //OLD: private Map<Integer, UUID> referenceMap = new HashMap<Integer, UUID>();
  62         private MapWrapper<Agent> authorStore= new MapWrapper<Agent>(null);
  63         private MapWrapper<ReferenceBase> referenceStore= new MapWrapper<ReferenceBase>(null);
  64         private MapWrapper<TaxonNameBase> taxonNameStore = new MapWrapper<TaxonNameBase>(null);
  65         private MapWrapper<TaxonBase> taxonStore = new MapWrapper<TaxonBase>(null);
  66
  67
  68         /**
  69          * Executes the whole
  70          */
  71         public boolean doImport(Source source, CdmApplicationController cdmApp){
  72                 if (source == null || cdmApp == null){
  73                         throw new NullPointerException("Source and CdmApplicationController must not be null");
  74                 }
  75                 this.source = source;
  76                 this.cdmApp = cdmApp;
  77
  78                 //make and save Authors
  79                 if (false){
  80                         if (! BerlinModelAuthorIO.invoke(source, cdmApp, deleteAll, authorStore)){
  81                                 return false;
  82                         }
  83                 }else{
  84                         referenceStore = null;
  85                 }
  86                 //make and save References
  87                 if (false){
  88                         if (! BerlinModelReferenceIO.invoke(source, cdmApp, deleteAll, referenceStore, authorStore)){
  89                                 return false;
  90                         }
  91                 }else{
  92                         referenceStore = null;
  93                 }
  94
  95                 //make and save Names
  96                 if (! BerlinModelTaxonNameIO.invoke(source, cdmApp, deleteAll, taxonNameStore, referenceStore, authorStore)){
  97                         return false;
  98                 }
  99
 100                 if(true){
 101                         return true;
 102                 }
 103
 104                 //make and save Taxa
 105                 if (! BerlinModelTaxonIO.invoke(source, cdmApp, deleteAll, taxonStore, taxonNameStore, referenceStore)){
 106                         return false;
 107                 }
 108
 109                 //make and save Facts
 110                 makeRelTaxa();
 111
 112                 //make and save Facts
 113                 makeFacts();
 114
 115                 if (false){
 116                         //make and save publications
 117 /*                              makePublications(root);
 118                                 saveToXml(root.getChild("Publications", nsTcs), outputPath, outputFileName + "Publications", format);
 119
 120                                 saveToXml(root.getChild("TaxonNames", nsTcs), outputPath, outputFileName + "_TaxonNames", format);
 121
 122                                 //make and save Concepts
 123                                 makeConcepts(root);
 124                                 saveToXml(root.getChild("TaxonConcepts", nsTcs), outputPath, outputFileName + "_TaxonConcepts", format);
 125 */              }
 126                 return true;
 127         }
 128
 129         /**
 130          * @return
 131          */
 132         private boolean makeRelTaxa(){
 133                 String dbAttrName;
 134                 String cdmAttrName;
 135
 136                 logger.info("start makeTaxonRelationships ...");
 137                 logger.warn("RelTaxa not yet implemented !!");
 138
 139                 ITaxonService taxonService = cdmApp.getTaxonService();
 140                 boolean delete = deleteAll;
 141
 142 //              if (delete){
 143 //                      List<Agent> listAllAgents =  agentService.getAllAgents(0, 1000);
 144 //                      while(listAllAgents.size() > 0 ){
 145 //                              for (Agent name : listAllAgents ){
 146 //                                      //FIXME
 147 //                                      //nameService.remove(name);
 148 //                              }
 149 //                              listAllAgents =  agentService.getAllAgents(0, 1000);
 150 //                      }
 151 //              }
 152                 try {
 153                         //get data from database
 154                         String strQuery =
 155                                         " SELECT *  " +
 156                     " FROM RelPTaxon Join Taxon1 Join Taxon2" ;
 157                         ResultSet rs = source.getResultSet(strQuery) ;
 158                         int i = 0;
 159                         //for each reference
 160                         while (rs.next()){
 161
 162                                 if ((i++ % modCount) == 0){ logger.info("RelPTaxa handled: " + (i-1));}
 163
 164
 165                                 int taxon1Id = rs.getInt("taxon1Id");
 166                                 int taxon2Id = rs.getInt("taxon2Id");
 167                                 int factId = rs.getInt("factId");
 168                                 int relTypeFk = rs.getInt("relTypeFk");
 169
 170                                 TaxonBase taxon1 = taxonStore.get(taxon1Id);
 171                                 TaxonBase taxon2 = taxonStore.get(taxon2Id);
 172
 173                                 //TODO
 174                                 ReferenceBase citation = null;
 175                                 String microcitation = null;
 176
 177
 178                                 if (relTypeFk == IS_INCLUDED_IN){
 179                                         ((Taxon)taxon2).addTaxonomicChild((Taxon)taxon1, citation, microcitation);
 180                                 }else if (relTypeFk == IS_SYNONYM_OF){
 181                                         ((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.SYNONYM_OF());
 182                                 }else if (relTypeFk == IS_HOMOTYPIC_SYNONYM_OF){
 183                                         ((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.HOMOTYPIC_SYNONYM_OF());
 184                                 }else if (relTypeFk == IS_HETEROTYPIC_SYNONYM_OF){
 185                                         ((Taxon)taxon2).addSynonym((Synonym)taxon1, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
 186                                 }else if (relTypeFk == IS_MISAPPLIED_NAME_OF){
 187                                         ((Taxon)taxon2).addMisappliedName((Taxon)taxon1, citation, microcitation);
 188                                 }else {
 189                                         //TODO
 190                                         logger.warn("TaxonRelationShipType " + relTypeFk + " not yet implemented");
 191                                 }
 192
 193
 194                         //....
 195
 196
 197
 198                         }
 199                         logger.info("end makeFacts ...");
 200                         return true;
 201                 } catch (SQLException e) {
 202                         logger.error("SQLException:" +  e);
 203                         return false;
 204                 }
 205         }
 206
 207
 208         /**
 209          * @return
 210          */
 211         private boolean makeFacts(){
 212                 String dbAttrName;
 213                 String cdmAttrName;
 214
 215                 logger.info("start makeFacts ...");
 216                 logger.warn("Facts not yet implemented !!");
 217
 218                 //IAgentService agentService = cdmApp.getAgentService();
 219                 boolean delete = deleteAll;
 220
 221 //              if (delete){
 222 //                      List<Agent> listAllAgents =  agentService.getAllAgents(0, 1000);
 223 //                      while(listAllAgents.size() > 0 ){
 224 //                              for (Agent name : listAllAgents ){
 225 //                                      //FIXME
 226 //                                      //nameService.remove(name);
 227 //                              }
 228 //                              listAllAgents =  agentService.getAllAgents(0, 1000);
 229 //                      }
 230 //              }
 231                 try {
 232                         //get data from database
 233                         String strQuery =
 234                                         " SELECT *  " +
 235                     " FROM Facts " ;
 236                         ResultSet rs = source.getResultSet(strQuery) ;
 237                         int i = 0;
 238                         //for each reference
 239                         while (rs.next()){
 240
 241                                 if ((i++ % modCount) == 0){ logger.info("Facts handled: " + (i-1));}
 242
 243                                 //create TaxonName element
 244                                 int factId = rs.getInt("factId");
 245
 246                         //....
 247
 248
 249
 250                         }
 251                         logger.info("end makeFacts ...");
 252                         return true;
 253                 } catch (SQLException e) {
 254                         logger.error("SQLException:" +  e);
 255                         return false;
 256                 }
 257         }
 258
 259
 260
 261
 262
 263
 264 }