cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/berlinModel/in/BerlinModelCommonNamesImport.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.HashSet;
  15 import java.util.Map;
  16 import java.util.Set;
  17
  18 import org.apache.log4j.Logger;
  19 import org.springframework.stereotype.Component;
  20
  21 import eu.etaxonomy.cdm.io.berlinModel.BerlinModelTransformer;
  22 import eu.etaxonomy.cdm.io.common.ICdmIO;
  23 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  24 import eu.etaxonomy.cdm.io.common.MapWrapper;
  25 import eu.etaxonomy.cdm.io.common.Source;
  26 import eu.etaxonomy.cdm.model.common.CdmBase;
  27 import eu.etaxonomy.cdm.model.description.Distribution;
  28 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
  29 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  30 import eu.etaxonomy.cdm.model.location.NamedArea;
  31 import eu.etaxonomy.cdm.model.location.TdwgArea;
  32 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  33 import eu.etaxonomy.cdm.model.taxon.Taxon;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  35 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  36
  37 /**
  38  * @author a.mueller
  39  * @created 20.03.2008
  40  * @version 1.0
  41  */
  42 @Component
  43 public class BerlinModelCommonNamesImport  extends BerlinModelImportBase {
  44         private static final Logger logger = Logger.getLogger(BerlinModelCommonNamesImport.class);
  45
  46         private static int modCount = 10000;
  47
  48         public BerlinModelCommonNamesImport(){
  49                 super();
  50         }
  51
  52         /* (non-Javadoc)
  53          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  54          */
  55         @Override
  56         protected boolean doCheck(IImportConfigurator config){
  57                 boolean result = true;
  58                 logger.warn("Checking for Occurrence not yet implemented");
  59                 //result &= checkArticlesWithoutJournal(bmiConfig);
  60                 //result &= checkPartOfJournal(bmiConfig);
  61
  62                 return result;
  63         }
  64
  65         /* (non-Javadoc)
  66          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  67          */
  68         @Override
  69         protected boolean doInvoke(BerlinModelImportState<BerlinModelImportConfigurator> state){
  70
  71                 MapWrapper<TaxonBase> taxonMap = (MapWrapper<TaxonBase>)state.getStore(ICdmIO.TAXON_STORE);
  72                 MapWrapper<ReferenceBase> referenceMap = (MapWrapper<ReferenceBase>)state.getStore(ICdmIO.REFERENCE_STORE);
  73                 BerlinModelImportConfigurator config = state.getConfig();
  74
  75                 if (true){
  76                         return false;
  77                 }
  78
  79                 Set<TaxonBase> taxonStore = new HashSet<TaxonBase>();
  80                 Source source = config.getSource();
  81
  82                 String dbAttrName;
  83                 String cdmAttrName;
  84
  85                 logger.info("start make occurrences ...");
  86
  87                 boolean delete = config.isDeleteAll();
  88
  89                 try {
  90                         //get data from database
  91                         String strQuery =
  92                                         " SELECT PTaxon.RIdentifier, emOccurrence.OccurrenceId, emOccurSumCat.emOccurSumCatId, emOccurSumCat.Short, emOccurSumCat.Description, " +
  93                         " emOccurSumCat.OutputCode, emArea.AreaId, emArea.EMCode, emArea.ISOCode, emArea.TDWGCode, emArea.Unit, " +
  94                         " emArea.Status, emArea.OutputOrder, emArea.eur, emArea.EuroMedArea " +
  95                     " FROM emOccurrence INNER JOIN " +
  96                         " emArea ON emOccurrence.AreaFk = emArea.AreaId INNER JOIN " +
  97                         " PTaxon ON emOccurrence.PTNameFk = PTaxon.PTNameFk AND emOccurrence.PTRefFk = PTaxon.PTRefFk LEFT OUTER JOIN " +
  98                         " emOccurSumCat ON emOccurrence.SummaryStatus = emOccurSumCat.emOccurSumCatId LEFT OUTER JOIN " +
  99                         " emOccurrenceSource ON emOccurrence.OccurrenceId = emOccurrenceSource.OccurrenceFk " +
 100                     " WHERE (1=1)";
 101                         ResultSet rs = source.getResultSet(strQuery) ;
 102
 103                         int i = 0;
 104                         //for each reference
 105                         while (rs.next()){
 106
 107                                 if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Facts handled: " + (i-1));}
 108
 109                                 int occurrenceId = rs.getInt("OccurrenceId");
 110                                 int taxonId = rs.getInt("RIdentifier");
 111                                 String tdwgCode = rs.getString("TDWGCode");
 112                                 Integer emStatusId = (Integer)rs.getObject("emOccurSumCatId");
 113
 114
 115                                 TaxonBase taxonBase = taxonMap.get(taxonId);
 116                                 if (taxonBase != null){
 117                                         try {
 118
 119                                                 PresenceAbsenceTermBase<?> status = null;
 120                                                 if (emStatusId != null){
 121                                                                 status = BerlinModelTransformer.occStatus2PresenceAbsence(emStatusId);
 122                                                 }
 123
 124                                                 NamedArea tdwgArea = TdwgArea.getAreaByTdwgLabel(tdwgCode);
 125
 126                                                         Taxon taxon;
 127                                                         if ( taxonBase instanceof Taxon ) {
 128                                                                 taxon = (Taxon) taxonBase;
 129                                                         }else{
 130                                                                 logger.warn("TaxonBase for Occurrence " + occurrenceId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
 131                                                                 continue;
 132                                                         }
 133
 134                                                         if (tdwgArea != null){
 135                                                                 Distribution distribution = Distribution.NewInstance(tdwgArea, status);
 136                                                                 //TODO only one description per taxon (for all EM distributions)
 137                                                                 TaxonDescription taxonDescription = TaxonDescription.NewInstance();
 138
 139                                                                 taxon.addDescription(taxonDescription);
 140                                                                 taxonStore.add(taxon);
 141                                                         }
 142
 143                                                 } catch (UnknownCdmTypeException e) {
 144                                                         // TODO Auto-generated catch block
 145                                                         e.printStackTrace();
 146                                                 }
 147
 148 //                                              TODO
 149 //                                              sources
 150 //                                              references
 151
 152
 153
 154 //                                      //commonNames -> TODO move to separate IO
 155 //                                      String commonNameString;
 156 //                                      if (taxon.getName() != null){
 157 //                                              commonNameString = "Common " + taxon.getName().getTitleCache();
 158 //                                      }else{
 159 //                                              commonNameString = "Common (null)";
 160 //                                      }
 161 //                                      Language language = bmiConfig.getFactLanguage();
 162 //                                      language = null;
 163 //                                      CommonTaxonName commonName = CommonTaxonName.NewInstance(commonNameString, language);
 164 //                                      taxonDescription.addElement(commonName);
 165
 166
 167
 168                                 }else{
 169                                         //TODO
 170                                         logger.warn("Taxon for Fact " + occurrenceId + " does not exist in store");
 171                                 }
 172                                 //put
 173                         }
 174                         logger.info("Taxa to save: " + taxonStore.size());
 175                         getTaxonService().saveTaxonAll(taxonStore);
 176
 177                         logger.info("end make occurrences ...");
 178                         return true;
 179                 } catch (SQLException e) {
 180                         logger.error("SQLException:" +  e);
 181                         return false;
 182                 }
 183
 184         }
 185
 186         /* (non-Javadoc)
 187          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 188          */
 189         protected boolean isIgnore(IImportConfigurator config){
 190                 return ! config.isDoOccurrence();
 191         }
 192
 193 }