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.HashMap;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Map;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.log4j.Logger;
  22 import org.springframework.stereotype.Component;
  23 import org.springframework.transaction.TransactionStatus;
  24
  25 import eu.etaxonomy.cdm.io.common.Source;
  26 import eu.etaxonomy.cdm.model.description.Distribution;
  27 import eu.etaxonomy.cdm.model.description.Feature;
  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.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33
  34
  35 /**
  36  * @author a.babadshanjan
  37  * @created 12.05.2009
  38  * @version 1.0
  39  */
  40 @Component
  41 public class FaunaEuropaeaDistributionImport extends FaunaEuropaeaImportBase {
  42         private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
  43
  44
  45         /* (non-Javadoc)
  46          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  47          */
  48         @Override
  49         protected boolean doCheck(FaunaEuropaeaImportState state) {
  50                 boolean result = true;
  51                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  52                 logger.warn("Checking for Distributions not yet fully implemented");
  53                 result &= checkReferenceStatus(fauEuConfig);
  54
  55                 return result;
  56         }
  57
  58         private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
  59                 boolean result = true;
  60 //              try {
  61                         Source source = fauEuConfig.getSource();
  62                         String sqlStr = "";
  63         //              ResultSet rs = source.getResultSet(sqlStr);
  64                         return result;
  65 //              } catch (SQLException e) {
  66 //                      e.printStackTrace();
  67 //                      return false;
  68 //              }
  69         }
  70
  71         /* (non-Javadoc)
  72          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  73          */
  74         @Override
  75         protected boolean doInvoke(FaunaEuropaeaImportState state) {
  76
  77                 int limit = state.getConfig().getLimitSave();
  78
  79                 /* Taxon store for retrieving taxa from and saving taxa to CDM */
  80                 List<TaxonBase> taxonList = null;
  81                 /* UUID store as input for retrieving taxa from CDM */
  82                 Set<UUID> taxonUuids = null;
  83                 /* Store to hold helper objects */
  84                 Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap = null;
  85
  86 //              Map<UUID, TaxonBase<?>> taxonMap = null;
  87 //              Set<TaxonBase<?>> taxonSet = null;
  88
  89                 TransactionStatus txStatus = null;
  90
  91                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  92                 Source source = fauEuConfig.getSource();
  93
  94                 String namespace = "Distribution";
  95                 boolean success = true;
  96
  97
  98                 //make not needed maps empty
  99 //              Map<String, MapWrapper<? extends CdmBase>> stores = state.getStores();
 100 //              MapWrapper<TeamOrPersonBase<?>> authorStore = (MapWrapper<TeamOrPersonBase<?>>)stores.get(ICdmIO.TEAM_STORE);
 101 //              authorStore.makeEmpty();
 102
 103                 if(logger.isInfoEnabled()) { logger.info("Start making distributions..."); }
 104
 105                 try {
 106                         String strQuery =
 107                                 " SELECT distribution.*, Area.*, Taxon.UUID " +
 108                                 " FROM distribution INNER JOIN " +
 109                 " Area ON distribution.dis_ara_id = Area.ara_id INNER JOIN " +
 110                 " Taxon ON distribution.dis_tax_id = Taxon.TAX_ID ";
 111
 112                         ResultSet rs = source.getResultSet(strQuery) ;
 113
 114                         int i = 0;
 115                         while (rs.next()) {
 116
 117                                 if ((i++ % limit) == 0) {
 118
 119                                         txStatus = startTransaction();
 120                                         taxonUuids = new HashSet<UUID>(limit);
 121                                         fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaDistributionTaxon>(limit);
 122 //                                      taxonSet = new HashSet<TaxonBase<?>>(limit);
 123
 124                                         if(logger.isInfoEnabled()) {
 125                                                 logger.info("i = " + i + " - Distribution import transaction started");
 126                                         }
 127                                 }
 128
 129                                 int taxonId = rs.getInt("dis_tax_id");
 130                                 int disId = rs.getInt("dis_id");
 131                                 int occStatusId = rs.getInt("dis_present");
 132                                 int areaId = rs.getInt("ara_id");
 133                                 String areaName = rs.getString("ara_name");
 134                                 String areaCode = rs.getString("ara_code");
 135                                 int extraLimital = rs.getInt("ara_extralimital");
 136                                 UUID currentTaxonUuid = null;
 137                                 if (resultSetHasColumn(rs,"UUID")){
 138                                         currentTaxonUuid = UUID.fromString(rs.getString("UUID"));
 139                                 } else {
 140                                         currentTaxonUuid = UUID.randomUUID();
 141                                 }
 142
 143                                 FaunaEuropaeaDistribution fauEuDistribution = new FaunaEuropaeaDistribution();
 144 //                              fauEuDistribution.setTaxonUuid(currentTaxonUuid);
 145 //                              fauEuDistribution.setTaxonId(taxonId);
 146                                 fauEuDistribution.setDistributionId(disId);
 147                                 fauEuDistribution.setOccurrenceStatusId(occStatusId);
 148                                 fauEuDistribution.setAreaId(areaId);
 149                                 fauEuDistribution.setAreaName(areaName);
 150                                 fauEuDistribution.setAreaCode(areaCode);
 151                                 fauEuDistribution.setExtraLimital(extraLimital);
 152
 153                                 if (!taxonUuids.contains(currentTaxonUuid)) {
 154                                         taxonUuids.add(currentTaxonUuid);
 155                                         FaunaEuropaeaDistributionTaxon fauEuDistributionTaxon =
 156                                                 new FaunaEuropaeaDistributionTaxon(currentTaxonUuid);
 157                                         fauEuTaxonMap.put(currentTaxonUuid, fauEuDistributionTaxon);
 158                                 } else {
 159                                         if (logger.isTraceEnabled()) {
 160                                                 logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
 161                                                 continue;
 162                                         }
 163                                 }
 164
 165                                 fauEuTaxonMap.get(currentTaxonUuid).addDistribution(fauEuDistribution);
 166
 167                                 if ((i % limit) == 0 && i != 1 ) {
 168
 169                                         try {
 170
 171                                                 taxonList = getTaxonService().findByUuid(taxonUuids);
 172
 173                                                 for (TaxonBase taxonBase : taxonList) {
 174
 175                                                         if (taxonBase != null) {
 176                                                                 Taxon taxon;
 177                                                                 if (taxonBase instanceof Taxon) {
 178                                                                         taxon = taxonBase.deproxy(taxonBase, Taxon.class);
 179                                                                 } else {
 180                                                                         logger.warn("TaxonBase (" + taxonId + " is not of type Taxon but: "
 181                                                                                         + taxonBase.getClass().getSimpleName());
 182                                                                         continue;
 183                                                                 }
 184
 185                                                                 TaxonDescription taxonDescription;
 186                                                                 Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
 187                                                                 if (descriptionSet.size() > 0) {
 188                                                                         taxonDescription = descriptionSet.iterator().next();
 189                                                                 } else {
 190                                                                         taxonDescription = TaxonDescription.NewInstance();
 191                                                                         taxon.addDescription(taxonDescription);
 192                                                                 }
 193
 194                                                                 UUID taxonUuid = taxonBase.getUuid();
 195                                                                 FaunaEuropaeaDistributionTaxon fauEuHelperTaxon = fauEuTaxonMap.get(taxonUuid);
 196
 197                                                                 for (FaunaEuropaeaDistribution fauEuHelperDistribution : fauEuHelperTaxon.getDistributions()) {
 198
 199                                                                         PresenceAbsenceTermBase<?> presenceAbsenceStatus
 200                                                                         = FaunaEuropaeaTransformer.occStatus2PresenceAbsence(fauEuHelperDistribution.getOccurrenceStatusId());
 201                                                                         NamedArea namedArea =
 202                                                                                 FaunaEuropaeaTransformer.areaId2TdwgArea(fauEuHelperDistribution);
 203
 204                                                                         Distribution newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
 205                                                                         newDistribution.setType(Feature.DISTRIBUTION());
 206                                                                         taxonDescription.addElement(newDistribution);
 207                                                                 }
 208                                                         }
 209                                                 }
 210                                                 if(logger.isInfoEnabled()) { logger.info("Saving taxa..."); }
 211
 212                                                 getTaxonService().saveTaxonAll(taxonList);
 213
 214                                                 taxonUuids = null;
 215                                                 taxonList = null;
 216                                                 fauEuTaxonMap = null;
 217                                                 commitTransaction(txStatus);
 218
 219                                         } catch (Exception e) {
 220                                                 logger.warn("An exception occurred when creating distribution with id " + disId);
 221                                                 e.printStackTrace();
 222                                         }
 223                                 }
 224                         }
 225                 } catch (SQLException e) {
 226                         logger.error("SQLException:" +  e);
 227                         return false;
 228                 }
 229                 if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
 230
 231                 return true;
 232         }
 233
 234
 235         /* (non-Javadoc)
 236          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 237          */
 238         protected boolean isIgnore(FaunaEuropaeaImportState state){
 239                 return !state.getConfig().isDoOccurrence();
 240         }
 241 }