cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/faunaEuropaea/FaunaEuropaeaDistributionImport.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.faunaEuropaea;
  11
  12 import java.sql.ResultSet;
  13 import java.sql.SQLException;
  14 import java.util.ArrayList;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Set;
  19
  20 import org.apache.log4j.Logger;
  21 import org.springframework.stereotype.Component;
  22 import org.springframework.transaction.TransactionStatus;
  23
  24 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  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.description.DescriptionElementBase;
  33 import eu.etaxonomy.cdm.model.description.Distribution;
  34 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
  35 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  36 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  37 import eu.etaxonomy.cdm.model.location.NamedArea;
  38 import eu.etaxonomy.cdm.model.location.TdwgArea;
  39 import eu.etaxonomy.cdm.model.reference.Generic;
  40 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  41 import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
  42 import eu.etaxonomy.cdm.model.taxon.Taxon;
  43 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  44 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  45
  46
  47 /**
  48  * @author a.babadshanjan
  49  * @created 12.05.2009
  50  * @version 1.0
  51  */
  52 @Component
  53 public class FaunaEuropaeaDistributionImport  extends FaunaEuropaeaImportBase {
  54         private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
  55
  56         private int modCount = 10000;
  57         /* Max number of references to be saved with one service call */
  58         private int limit = 20000; // TODO: Make configurable
  59
  60         /* (non-Javadoc)
  61          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  62          */
  63         @Override
  64         protected boolean doCheck(FaunaEuropaeaImportState state) {
  65                 boolean result = true;
  66                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  67                 logger.warn("Checking for Distributions not yet fully implemented");
  68                 result &= checkReferenceStatus(fauEuConfig);
  69
  70                 return result;
  71         }
  72
  73         private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
  74                 boolean result = true;
  75 //              try {
  76                         Source source = fauEuConfig.getSource();
  77                         String sqlStr = "";
  78                         ResultSet rs = source.getResultSet(sqlStr);
  79                         return result;
  80 //              } catch (SQLException e) {
  81 //                      e.printStackTrace();
  82 //                      return false;
  83 //              }
  84         }
  85
  86         /* (non-Javadoc)
  87          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  88          */
  89         @Override
  90         protected boolean doInvoke(FaunaEuropaeaImportState state) {
  91
  92                 Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
  93                 MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
  94                 TransactionStatus txStatus = null;
  95
  96                 //make not needed maps empty
  97 //              MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
  98 //              authorMap.makeEmpty();
  99
 100                 Set<TaxonBase> taxonMap = new HashSet<TaxonBase>();
 101
 102                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
 103                 Source source = fauEuConfig.getSource();
 104
 105                 String namespace = "Distribution";
 106                 boolean success = true;
 107
 108                 if(logger.isInfoEnabled()) { logger.info("Start making Distributions..."); }
 109
 110                 try {
 111                         String strQuery =
 112                                 " SELECT distribution.*, Area.* " +
 113                 " FROM distribution INNER JOIN Area ON distribution.dis_ara_id = Area.ara_id " +
 114                 " WHERE (1=1)";
 115
 116                         ResultSet rs = source.getResultSet(strQuery) ;
 117
 118                         int i = 0;
 119                         while (rs.next()) {
 120
 121                                 if ((i++ % modCount) == 0 && i!= 1 ) {
 122                                         if(logger.isInfoEnabled()) {
 123                                                 logger.info("Distributions handled: " + (i-1));
 124                                         }
 125                                 }
 126
 127                                 int disId = rs.getInt("dis_id");
 128                                 int taxonId = rs.getInt("dis_tax_id");
 129                                 int occStatusId = rs.getInt("dis_present");
 130
 131                                 TaxonBase<?> taxonBase = taxonStore.get(taxonId);
 132
 133                                 try {
 134                                 if (taxonBase != null) {
 135                                         Taxon taxon;
 136                                         if (taxonBase instanceof Taxon) {
 137                                                 taxon = (Taxon)taxonBase;
 138                                         } else {
 139                                                 logger.warn("TaxonBase (" + taxonId + " is not of type Taxon but: "
 140                                                                 + taxonBase.getClass().getSimpleName());
 141                                                 continue;
 142                                         }
 143
 144                                         TaxonDescription taxonDescription;
 145                                         Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
 146                                         if (descriptionSet.size() > 0) {
 147                                                 taxonDescription = descriptionSet.iterator().next();
 148                                         } else {
 149                                                 taxonDescription = TaxonDescription.NewInstance();
 150                                                 taxon.addDescription(taxonDescription);
 151                                         }
 152
 153                                 PresenceAbsenceTermBase<?> presenceAbsenceStatus
 154                                 = FaunaEuropaeaTransformer.occStatus2PresenceAbsence(occStatusId);
 155                                         NamedArea namedArea = FaunaEuropaeaTransformer.areaId2TdwgArea(rs);
 156
 157                                         Distribution newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
 158                                         taxonDescription.addElement(newDistribution);
 159
 160                                         //ImportHelper.setOriginalSource(reference, fauEuConfig.getSourceReference(), disId, namespace);
 161
 162 //                                      if (!refStore.containsId(refId)) {
 163 //                                              if (reference == null) {
 164 //                                                      logger.warn("Reference is null");
 165 //                                              }
 166 //                                              refStore.put(refId, reference);
 167 //                                      } else {
 168 //                                              logger.warn("Reference with duplicated ref_id (" + refId +
 169 //                                                              ") not imported.");
 170 //                                      }
 171                                         taxonMap.add(taxon);
 172                                 }
 173
 174                                 } catch (Exception e) {
 175                                         logger.warn("An exception occurred when creating distribution with id " + disId +
 176                                         ". Reference could not be saved.");
 177                                         e.printStackTrace();
 178                                 }
 179                         }
 180
 181                         if(logger.isInfoEnabled()) { logger.info("Saving distributions ..."); }
 182
 183                         if (state.getConfig().isUseTransactions()) {
 184                                 txStatus = startTransaction();
 185                         }
 186
 187                         success = saveTaxa(state, state.getHighestTaxonIndex(), state.getConfig().getLimitSave());
 188
 189                         if (state.getConfig().isUseTransactions()) {
 190                                 commitTransaction(txStatus);
 191                         }
 192
 193                         if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
 194
 195                         return true;
 196
 197                 } catch (SQLException e) {
 198                         logger.error("SQLException:" +  e);
 199                         return false;
 200                 }
 201         }
 202
 203
 204         /* (non-Javadoc)
 205          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 206          */
 207         protected boolean isIgnore(FaunaEuropaeaImportState state){
 208                 return !state.getConfig().isDoOccurrence();
 209         }
 210 }