cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelFactsImport.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.in;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.Collection;
  15 import java.util.HashSet;
  16 import java.util.Map;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.springframework.stereotype.Component;
  21
  22 import eu.etaxonomy.cdm.common.CdmUtils;
  23 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  24 import eu.etaxonomy.cdm.io.common.ICdmIO;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  26 import eu.etaxonomy.cdm.io.common.MapWrapper;
  27 import eu.etaxonomy.cdm.io.common.Source;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.common.Language;
  30 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  31 import eu.etaxonomy.cdm.model.description.Feature;
  32 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  33 import eu.etaxonomy.cdm.model.description.TextData;
  34 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  35 import eu.etaxonomy.cdm.model.taxon.Taxon;
  36 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  37 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  38
  39 /**
  40  * @author a.mueller
  41  * @created 20.03.2008
  42  * @version 1.0
  43  */
  44 @Component
  45 public class BerlinModelFactsImport  extends BerlinModelImportBase {
  46         private static final Logger logger = Logger.getLogger(BerlinModelFactsImport.class);
  47
  48         private int modCount = 10000;
  49
  50         public BerlinModelFactsImport(){
  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                 logger.warn("Checking for Facts not yet implemented");
  61                 //result &= checkArticlesWithoutJournal(bmiConfig);
  62                 //result &= checkPartOfJournal(bmiConfig);
  63
  64                 return result;
  65         }
  66
  67         private TermVocabulary<Feature> getFeatureVocabulary(){
  68                 try {
  69                         //TODO work around until service method works
  70                         TermVocabulary<Feature> featureVocabulary =  BerlinModelTransformer.factCategory2Feature(1).getVocabulary();
  71                         //TermVocabulary<Feature> vocabulary = getTermService().getVocabulary(vocabularyUuid);
  72                         return featureVocabulary;
  73                 } catch (UnknownCdmTypeException e) {
  74                         logger.error("Feature vocabulary not available. New vocabulary created");
  75                         return new TermVocabulary<Feature>() ;
  76                 }
  77         }
  78
  79         private MapWrapper<Feature> invokeFactCategories(BerlinModelImportConfigurator bmiConfig){
  80
  81 //              Map<Integer, Feature> featureMap = new HashMap<Integer, Feature>();
  82                 MapWrapper<Feature> result = bmiConfig.getFeatureMap();
  83
  84                 Source source = bmiConfig.getSource();
  85
  86
  87                 try {
  88                         //get data from database
  89                         String strQuery =
  90                                         " SELECT FactCategory.* " +
  91                                         " FROM FactCategory "+
  92                     " WHERE (1=1)";
  93                         ResultSet rs = source.getResultSet(strQuery) ;
  94
  95
  96                         TermVocabulary<Feature> featureVocabulary = getFeatureVocabulary();
  97                         int i = 0;
  98                         //for each reference
  99                         while (rs.next()){
 100
 101                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("FactCategories handled: " + (i-1));}
 102
 103                                 int factCategoryId = rs.getInt("factCategoryId");
 104                                 String factCategory = rs.getString("factCategory");
 105
 106
 107                                 Feature feature;
 108                                 try {
 109                                         feature = BerlinModelTransformer.factCategory2Feature(factCategoryId);
 110                                 } catch (UnknownCdmTypeException e) {
 111                                         logger.warn("New Feature (FactCategoryId: " + factCategoryId + ")");
 112                                         feature = Feature.NewInstance(factCategory, factCategory, null);
 113                                         feature.setVocabulary(featureVocabulary);
 114                                         feature.setSupportsTextData(true);
 115                                         //TODO
 116 //                                      MaxFactNumber   int     Checked
 117 //                                      ExtensionTableName      varchar(100)    Checked
 118 //                                      Description     nvarchar(1000)  Checked
 119 //                                      locExtensionFormName    nvarchar(80)    Checked
 120 //                                      RankRestrictionFk       int     Checked
 121                                 }
 122
 123                         //      featureMap.put(factCategoryId, feature);
 124                                 result.put(factCategoryId, feature);
 125
 126                         }
 127                         Collection<Feature> col = result.getAllValues();
 128                         getTermService().saveTermsAll(col);
 129                         return result;
 130                 } catch (SQLException e) {
 131                         logger.error("SQLException:" +  e);
 132                         return null;
 133                 }
 134
 135         }
 136
 137
 138         /* (non-Javadoc)
 139          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
 140          */
 141         @Override
 142         protected boolean doInvoke(BerlinModelImportState<BerlinModelImportConfigurator> state){
 143                 boolean result = true;
 144
 145                 MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE);
 146                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)state.getStore(ICdmIO.REFERENCE_STORE);
 147                 MapWrapper<ReferenceBase> nomRefMap = (MapWrapper<ReferenceBase>)state.getStore(ICdmIO.NOMREF_STORE);
 148
 149                 Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();
 150
 151                 BerlinModelImportConfigurator config = state.getConfig();
 152                 Source source = config.getSource();
 153
 154                 logger.info("start makeFacts ...");
 155
 156                 MapWrapper<Feature> featureMap = invokeFactCategories(config);
 157
 158                 //for testing only
 159                 //TaxonBase taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(null), null);
 160
 161
 162                 try {
 163                         //get data from database
 164                         String strQuery =
 165                                         " SELECT Fact.*, PTaxon.RIdentifier as taxonId, RefDetail.Details " +
 166                                         " FROM Fact " +
 167                         " INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk " +
 168                         " LEFT OUTER JOIN RefDetail ON Fact.FactRefDetailFk = RefDetail.RefDetailId AND Fact.FactRefFk = RefDetail.RefFk " +
 169                         " WHERE (1=1)";
 170                         ResultSet rs = source.getResultSet(strQuery) ;
 171
 172                         int i = 0;
 173                         //for each reference
 174                         while (rs.next()){
 175                                 try{
 176                                         if ((i++ % modCount) == 0){ logger.info("Facts handled: " + (i-1));}
 177
 178                                         //Map<String, Object> valueMap = getValueMap(rs);
 179
 180                                         int factId = rs.getInt("factId");
 181
 182
 183                                         Object taxonIdObj = rs.getObject("taxonId");
 184                                         int taxonId = rs.getInt("taxonId");
 185                                         Object factRefFkObj = rs.getObject("factRefFk");
 186                                         int factRefFk = rs.getInt("factRefFk");
 187                                         Object categoryFkObj = rs.getObject("factCategoryFk");
 188                                         Integer categoryFk = rs.getInt("factCategoryFk");
 189
 190                                         String details = rs.getString("Details");
 191         //                              int ptDesignationRefFk = rs.getInt("PTDesignationRefFk");
 192         //                              String ptDesignation details = rs.getInt("PTDesignationRefDetailFk");
 193                                         String fact = CdmUtils.Nz(rs.getString("Fact"));
 194                                         String notes = CdmUtils.Nz(rs.getString("notes"));
 195
 196
 197
 198                                         TaxonBase taxonBase;
 199                                         if (taxonIdObj != null){
 200                                                 taxonBase = taxonMap.get(taxonId);
 201                                         }else{
 202                                                 taxonBase = null;
 203                                         }
 204                                         Feature feature;
 205                                         if (categoryFkObj != null){
 206                                                 feature = featureMap.get(categoryFk);
 207                                         }else{
 208                                                 feature = null;
 209                                         }
 210
 211                                         if (taxonBase != null){
 212                                                 Taxon taxon;
 213                                                 if ( taxonBase instanceof Taxon ) {
 214                                                         taxon = (Taxon) taxonBase;
 215                                                 }else{
 216                                                         logger.warn("TaxonBase " + (taxonIdObj==null?"(null)":taxonIdObj) + " for Fact " + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
 217                                                         continue;
 218                                                 }
 219
 220                                                 TaxonDescription taxonDescription;
 221                                                 Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
 222                                                 if (descriptionSet.size() > 0) {
 223                                                         taxonDescription = descriptionSet.iterator().next();
 224                                                 }else{
 225                                                         taxonDescription = TaxonDescription.NewInstance();
 226                                                         taxon.addDescription(taxonDescription);
 227                                                 }
 228
 229                                                 //textData
 230                                                 TextData textData = TextData.NewInstance();
 231                                                 //TODO textData.putText(fact, bmiConfig.getFactLanguage());  //doesn't work because  bmiConfig.getFactLanguage() is not not a persistent Language Object
 232                                                 //throws  in thread "main" org.springframework.dao.InvalidDataAccessApiUsageException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language; nested exception is org.hibernate.TransientObjectException: object references an unsaved transient instance - save the transient instance before flushing: eu.etaxonomy.cdm.model.common.Language
 233
 234                                                 //for diptera database
 235                                                 if (categoryFk == 99 && notes.contains("<OriginalName>")){
 236                                                         notes = notes.replaceAll("<OriginalName>", "");
 237                                                         notes = notes.replaceAll("</OriginalName>", "");
 238                                                         fact = notes + ": " +  fact ;
 239                                                 }
 240                                                 textData.putText(fact, Language.DEFAULT());
 241                                                 textData.setType(feature);
 242
 243                                                 //
 244                                                 ReferenceBase citation;
 245                                                 if (factRefFkObj != null){
 246                                                         citation = referenceMap.get(factRefFk);
 247                                                         if (citation == null){
 248                                                                 citation = nomRefMap.get(factRefFk);
 249                                                         }
 250                                                         if (citation == null && (factRefFk != 0)){
 251                                                                 logger.warn("Citation not found in referenceMap: " + factRefFk);
 252                                                         }
 253                                                 }else{
 254                                                         citation = null;
 255                                                 }
 256
 257
 258                                                 textData.setCitation(citation);
 259                                                 textData.setCitationMicroReference(details);
 260                                                 taxonDescription.addElement(textData);
 261
 262
 263 //                                              if (categoryFkObj == FACT_DESCRIPTION){
 264 //                                                      //;
 265 //                                              }else if (categoryFkObj == FACT_OBSERVATION){
 266 //                                                      //;
 267 //                                              }else if (categoryFkObj == FACT_DISTRIBUTION_EM){
 268 //                                                      //
 269 //                                              }else {
 270 //                                                      //TODO
 271 //                                                      //logger.warn("FactCategory " + categoryFk + " not yet implemented");
 272 //                                              }
 273
 274                                                 //TODO
 275                                                 //References
 276                                                 //factId,
 277
 278                                                 //etc.
 279                                                 doCreatedUpdatedNotes(config, textData, rs, "Fact");
 280
 281
 282                                                 taxonStore.add(taxon);
 283                                         }else{
 284                                                 //TODO
 285                                                 logger.warn("Taxon for Fact " + factId + " does not exist in store");
 286                                         }
 287                                 } catch (RuntimeException re){
 288                                         logger.error("A runtime exception occurred during the facts import");
 289                                         result = false;
 290                                         throw re;
 291                                 }
 292                                 //put
 293                         }
 294                         logger.info("Facts handled: " + (i-1));
 295                         logger.info("Taxa to save: " + taxonStore.size());
 296                         getTaxonService().saveTaxonAll(taxonStore);
 297
 298                         logger.info("end makeFacts ...");
 299                         return result;
 300                 } catch (SQLException e) {
 301                         logger.error("SQLException:" +  e);
 302                         return false;
 303                 }
 304
 305         }
 306
 307         /* (non-Javadoc)
 308          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 309          */
 310         protected boolean isIgnore(IImportConfigurator config){
 311                 return ! config.isDoFacts();
 312         }
 313
 314 }