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
  23 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  24 import eu.etaxonomy.cdm.io.common.ICdmIO;
  25 import eu.etaxonomy.cdm.io.common.IImportConfigurator;
  26 import eu.etaxonomy.cdm.io.common.ImportHelper;
  27 import eu.etaxonomy.cdm.io.common.MapWrapper;
  28 import eu.etaxonomy.cdm.io.common.Source;
  29 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  30 import eu.etaxonomy.cdm.model.common.CdmBase;
  31 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  32 import eu.etaxonomy.cdm.model.description.Distribution;
  33 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
  34 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  35 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  36 import eu.etaxonomy.cdm.model.location.NamedArea;
  37 import eu.etaxonomy.cdm.model.location.TdwgArea;
  38 import eu.etaxonomy.cdm.model.reference.Generic;
  39 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  40 import eu.etaxonomy.cdm.model.reference.StrictReferenceBase;
  41 import eu.etaxonomy.cdm.model.taxon.Taxon;
  42 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  43 import eu.etaxonomy.cdm.strategy.exceptions.UnknownCdmTypeException;
  44
  45
  46 /**
  47  * @author a.babadshanjan
  48  * @created 12.05.2009
  49  * @version 1.0
  50  */
  51 @Component
  52 public class FaunaEuropaeaDistributionImport  extends FaunaEuropaeaImportBase {
  53         private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
  54
  55         private int modCount = 10000;
  56         /* Max number of references to be saved with one service call */
  57         private int limit = 20000; // TODO: Make configurable
  58
  59         /* (non-Javadoc)
  60          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  61          */
  62         @Override
  63         protected boolean doCheck(IImportConfigurator config) {
  64                 boolean result = true;
  65                 FaunaEuropaeaImportConfigurator fauEuConfig = (FaunaEuropaeaImportConfigurator)config;
  66                 logger.warn("Checking for Distributions not yet fully implemented");
  67                 result &= checkReferenceStatus(fauEuConfig);
  68
  69                 return result;
  70         }
  71
  72         private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
  73                 boolean result = true;
  74 //              try {
  75                         Source source = fauEuConfig.getSource();
  76                         String sqlStr = "";
  77                         ResultSet rs = source.getResultSet(sqlStr);
  78                         return result;
  79 //              } catch (SQLException e) {
  80 //                      e.printStackTrace();
  81 //                      return false;
  82 //              }
  83         }
  84
  85         /* (non-Javadoc)
  86          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  87          */
  88         @Override
  89         protected boolean doInvoke(IImportConfigurator config,
  90                         Map<String, MapWrapper<? extends CdmBase>> stores) {
  91
  92                 MapWrapper<TaxonBase> taxonStore = (MapWrapper<TaxonBase>)stores.get(ICdmIO.TAXON_STORE);
  93
  94                 //make not needed maps empty
  95 //              MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
  96 //              authorMap.makeEmpty();
  97
  98                 Set<TaxonBase> taxonMap = new HashSet<TaxonBase>();
  99
 100                 FaunaEuropaeaImportConfigurator fauEuConfig = (FaunaEuropaeaImportConfigurator)config;
 101                 Source source = fauEuConfig.getSource();
 102
 103                 String namespace = "Distribution";
 104                 boolean success = true;
 105
 106                 if(logger.isInfoEnabled()) { logger.info("Start making Distributions..."); }
 107
 108                 try {
 109                         String strQuery =
 110                                 " SELECT distribution.*, Area.* " +
 111                 " FROM distribution INNER JOIN Area ON distribution.dis_ara_id = Area.ara_id " +
 112                 " WHERE (1=1)";
 113
 114                         ResultSet rs = source.getResultSet(strQuery) ;
 115
 116                         int i = 0;
 117                         while (rs.next()) {
 118
 119                                 if ((i++ % modCount) == 0 && i!= 1 ) {
 120                                         if(logger.isInfoEnabled()) {
 121                                                 logger.info("Distributions handled: " + (i-1));
 122                                         }
 123                                 }
 124
 125                                 int disId = rs.getInt("dis_id");
 126                                 int taxonId = rs.getInt("dis_tax_id");
 127                                 int occStatusId = rs.getInt("ara_id");
 128
 129                                 TaxonBase<?> taxonBase = taxonStore.get(taxonId);
 130
 131                                 try {
 132                                 if (taxonBase != null) {
 133                                         Taxon taxon;
 134                                         if (taxonBase instanceof Taxon) {
 135                                                 taxon = (Taxon)taxonBase;
 136                                         } else {
 137                                                 logger.warn("TaxonBase (" + taxonId + " is not of type Taxon but: "
 138                                                                 + taxonBase.getClass().getSimpleName());
 139                                                 continue;
 140                                         }
 141
 142                                         TaxonDescription taxonDescription;
 143                                         Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
 144                                         if (descriptionSet.size() > 0) {
 145                                                 taxonDescription = descriptionSet.iterator().next();
 146                                         } else {
 147                                                 taxonDescription = TaxonDescription.NewInstance();
 148                                                 taxon.addDescription(taxonDescription);
 149                                         }
 150
 151                                 PresenceAbsenceTermBase<?> presenceAbsenceStatus
 152                                 = FaunaEuropaeaTransformer.occStatus2PresenceAbsence(occStatusId);
 153                                         NamedArea namedArea = FaunaEuropaeaTransformer.areaId2TdwgArea(rs);
 154
 155                                         Distribution newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
 156                                         taxonDescription.addElement(newDistribution);
 157
 158                                         //ImportHelper.setOriginalSource(reference, fauEuConfig.getSourceReference(), disId, namespace);
 159
 160 //                                      if (!refStore.containsId(refId)) {
 161 //                                              if (reference == null) {
 162 //                                                      logger.warn("Reference is null");
 163 //                                              }
 164 //                                              refStore.put(refId, reference);
 165 //                                      } else {
 166 //                                              logger.warn("Reference with duplicated ref_id (" + refId +
 167 //                                                              ") not imported.");
 168 //                                      }
 169                                         taxonMap.add(taxon);
 170                                 }
 171
 172                                 } catch (Exception e) {
 173                                         logger.warn("An exception occurred when creating distribution with id " + disId +
 174                                         ". Reference could not be saved.");
 175                                 }
 176                         }
 177
 178                         if(logger.isInfoEnabled()) { logger.info("Saving distributions ..."); }
 179
 180                         // save taxa
 181                         getTaxonService().saveTaxonAll(taxonMap);
 182
 183                         if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
 184
 185                         return true;
 186
 187                 } catch (SQLException e) {
 188                         logger.error("SQLException:" +  e);
 189                         return false;
 190                 }
 191         }
 192
 193
 194         /* (non-Javadoc)
 195          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 196          */
 197         protected boolean isIgnore(IImportConfigurator config){
 198                 return (config.getDoReferences() == IImportConfigurator.DO_REFERENCES.NONE);
 199         }
 200 }