cdm-pesi/src/main/java/eu/etaxonomy/cdm/io/pesi/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.pesi.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.io.profiler.ProfilerController;
  27 import eu.etaxonomy.cdm.model.description.Distribution;
  28 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
  29 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  30 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  31 import eu.etaxonomy.cdm.model.location.NamedArea;
  32 import eu.etaxonomy.cdm.model.taxon.Taxon;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  34 import com.yourkit.api.Controller;
  35
  36
  37 /**
  38  * @author a.babadshanjan
  39  * @created 12.05.2009
  40  * @version 1.0
  41  */
  42 @Component
  43 public class FaunaEuropaeaDistributionImport extends FaunaEuropaeaImportBase {
  44         private static final Logger logger = Logger.getLogger(FaunaEuropaeaDistributionImport.class);
  45
  46
  47         /* (non-Javadoc)
  48          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IImportConfigurator)
  49          */
  50         @Override
  51         protected boolean doCheck(FaunaEuropaeaImportState state) {
  52                 boolean result = true;
  53                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
  54                 logger.warn("Checking for Distributions not yet fully implemented");
  55                 result &= checkReferenceStatus(fauEuConfig);
  56
  57                 return result;
  58         }
  59
  60         private boolean checkReferenceStatus(FaunaEuropaeaImportConfigurator fauEuConfig) {
  61                 boolean result = true;
  62 //              try {
  63                         Source source = fauEuConfig.getSource();
  64                         String sqlStr = "";
  65         //              ResultSet rs = source.getResultSet(sqlStr);
  66                         return result;
  67 //              } catch (SQLException e) {
  68 //                      e.printStackTrace();
  69 //                      return false;
  70 //              }
  71         }
  72
  73         /* (non-Javadoc)
  74          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IImportConfigurator, eu.etaxonomy.cdm.api.application.CdmApplicationController, java.util.Map)
  75          */
  76         /* (non-Javadoc)
  77          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doInvoke(eu.etaxonomy.cdm.io.common.IoStateBase)
  78          */
  79         @Override
  80         protected void doInvoke(FaunaEuropaeaImportState state) {
  81                 /*
  82                 logger.warn("Start distribution doInvoke");
  83                 ProfilerController.memorySnapshot();
  84                 */
  85                 int limit = state.getConfig().getLimitSave();
  86                 UUID noDataUuid;
  87                 /* Taxon store for retrieving taxa from and saving taxa to CDM */
  88                 List<TaxonBase> taxonList = null;
  89                 /* UUID store as input for retrieving taxa from CDM */
  90                 Set<UUID> taxonUuids = null;
  91                 /* Store to hold helper objects */
  92                 Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap = null;
  93
  94
  95                 TransactionStatus txStatus = null;
  96
  97                 //txStatus = startTransaction();
  98                 noDataUuid = getTermService().save(PresenceTerm.NewInstance("no data", "no data", "nod"));
  99                 //commitTransaction(txStatus);
 100
 101                 FaunaEuropaeaTransformer.setUUIDs(noDataUuid);
 102
 103                 txStatus = null;
 104
 105                 FaunaEuropaeaImportConfigurator fauEuConfig = state.getConfig();
 106                 Source source = fauEuConfig.getSource();
 107
 108         int i = 0;
 109
 110                 String selectCount =
 111                         " SELECT count(*) ";
 112
 113                 String selectColumns =
 114                         " SELECT distribution.*, Area.*, Taxon.UUID ";
 115
 116                 String fromClause =
 117                         " FROM distribution INNER JOIN " +
 118             " Area ON distribution.dis_ara_id = Area.ara_id INNER JOIN " +
 119             " Taxon ON distribution.dis_tax_id = Taxon.TAX_ID ";
 120                 String orderBy = " ORDER BY distribution.dis_tax_id";
 121
 122                 String countQuery =
 123                         selectCount + fromClause;
 124
 125                 String selectQuery =
 126                         selectColumns + fromClause + orderBy;
 127
 128
 129
 130                 if(logger.isInfoEnabled()) { logger.info("Start making distributions..."); }
 131
 132                 try {
 133                         ResultSet rs = source.getResultSet(countQuery);
 134                         rs.next();
 135                         int count = rs.getInt(1);
 136
 137                         rs = source.getResultSet(selectQuery);
 138
 139                         if (logger.isInfoEnabled()) {
 140                                 logger.info("Number of rows: " + count);
 141                                 logger.info("Count Query: " + countQuery);
 142                                 logger.info("Select Query: " + selectQuery);
 143                         }
 144
 145                         //int taxonId;
 146
 147                         while (rs.next()) {
 148                                 if ((i++ % limit) == 0) {
 149
 150                                         txStatus = startTransaction();
 151                                         taxonUuids = new HashSet<UUID>(limit);
 152                                         fauEuTaxonMap = new HashMap<UUID, FaunaEuropaeaDistributionTaxon>(limit);
 153
 154                                         if(logger.isInfoEnabled()) {
 155                                                 logger.info("i = " + i + " - Distribution import transaction started");
 156                                         }
 157                                 }
 158
 159                                 //taxonId = rs.getInt("dis_tax_id");
 160                                 int disId = rs.getInt("dis_id");
 161                                 int occStatusId = rs.getInt("dis_present");
 162                                 int areaId = rs.getInt("ara_id");
 163                                 String areaName = rs.getString("ara_name");
 164                                 String areaCode = rs.getString("ara_code");
 165                                 int extraLimital = rs.getInt("ara_extralimital");
 166                                 UUID currentTaxonUuid = null;
 167                                 if (resultSetHasColumn(rs,"UUID")){
 168                                         currentTaxonUuid = UUID.fromString(rs.getString("UUID"));
 169                                 } else {
 170                                         currentTaxonUuid = UUID.randomUUID();
 171                                 }
 172
 173                                 FaunaEuropaeaDistribution fauEuDistribution = new FaunaEuropaeaDistribution();
 174                                 fauEuDistribution.setDistributionId(disId);
 175                                 fauEuDistribution.setOccurrenceStatusId(occStatusId);
 176                                 fauEuDistribution.setAreaId(areaId);
 177                                 fauEuDistribution.setAreaName(areaName);
 178                                 fauEuDistribution.setAreaCode(areaCode);
 179                                 fauEuDistribution.setExtraLimital(extraLimital);
 180
 181                                 if (!taxonUuids.contains(currentTaxonUuid)) {
 182                                         taxonUuids.add(currentTaxonUuid);
 183                                         FaunaEuropaeaDistributionTaxon fauEuDistributionTaxon =
 184                                                 new FaunaEuropaeaDistributionTaxon(currentTaxonUuid);
 185                                         fauEuTaxonMap.put(currentTaxonUuid, fauEuDistributionTaxon);
 186                                         fauEuDistributionTaxon = null;
 187                                 } else {
 188                                         if (logger.isTraceEnabled()) {
 189                                                 logger.trace("Taxon (" + currentTaxonUuid + ") already stored.");
 190                                                 continue;
 191                                         }
 192                                 }
 193
 194                                 fauEuTaxonMap.get(currentTaxonUuid).addDistribution(fauEuDistribution);
 195
 196                                 if (((i % limit) == 0 && i != 1 ) || i == count ) {
 197
 198
 199
 200                                                 try {
 201                                                         commitTaxaAndDistribution(state,
 202                                                                         noDataUuid, taxonUuids, fauEuTaxonMap, txStatus);
 203
 204                                                 taxonUuids = null;
 205                                                 taxonList = null;
 206                                                 fauEuTaxonMap = null;
 207
 208
 209                                                 } catch (Exception e) {
 210                                                         logger.error("Commit of taxa and distributions failed");
 211                                                         e.printStackTrace();
 212                                                 }
 213
 214                                                 if(logger.isInfoEnabled()) {
 215                                                         logger.info("i = " + i + " - Transaction committed");
 216                                                 }
 217                                 }
 218
 219
 220                         }
 221                         if (taxonUuids != null){
 222                                 try {
 223                                         commitTaxaAndDistribution(state, noDataUuid, taxonUuids, fauEuTaxonMap, txStatus);
 224                                         taxonUuids = null;
 225                                         taxonList = null;
 226                                         fauEuTaxonMap = null;
 227                                 } catch (Exception e) {
 228                                         logger.error("Commit of taxa and distributions failed");
 229                                         logger.error(e.getMessage());
 230                                         e.printStackTrace();
 231                                 }
 232                         }
 233                 } catch (SQLException e) {
 234                         logger.error("SQLException:" +  e);
 235                         state.setUnsuccessfull();
 236                 }
 237                 if(logger.isInfoEnabled()) { logger.info("End making distributions..."); }
 238
 239                 return;
 240         }
 241
 242         private void commitTaxaAndDistribution(
 243                         FaunaEuropaeaImportState state, UUID noDataUuid,
 244                         Set<UUID> taxonUuids,
 245                         Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap,
 246                         TransactionStatus txStatus) throws Exception {
 247                 List<TaxonBase> taxonList;
 248                 taxonList = prepareTaxaAndDistribution(getTaxonService().find(taxonUuids), fauEuTaxonMap, noDataUuid, state);
 249
 250                 getTaxonService().save(taxonList);
 251                 commitTransaction(txStatus);
 252
 253         }
 254
 255         private List<TaxonBase> prepareTaxaAndDistribution(List<TaxonBase> taxonList, Map<UUID, FaunaEuropaeaDistributionTaxon> fauEuTaxonMap, UUID noData, FaunaEuropaeaImportState state) throws Exception{
 256
 257                 Distribution newDistribution = null;
 258                 NamedArea namedArea;
 259                 PresenceAbsenceTermBase<?> presenceAbsenceStatus;
 260                 FaunaEuropaeaDistributionTaxon fauEuHelperTaxon;
 261                 UUID taxonUuid;
 262                 TaxonDescription taxonDescription;
 263                 Taxon taxon;
 264                 for (TaxonBase taxonBase : taxonList) {
 265
 266                         if (taxonBase != null) {
 267
 268                                 if (taxonBase instanceof Taxon) {
 269                                         taxon = taxonBase.deproxy(taxonBase, Taxon.class);
 270                                 } else {
 271                                         logger.warn("TaxonBase (" + taxonBase.getId() + " is not of type Taxon but: "
 272                                                         + taxonBase.getClass().getSimpleName());
 273                                         continue;
 274                                 }
 275
 276
 277                                 Set<TaxonDescription> descriptionSet = taxon.getDescriptions();
 278                                 if (descriptionSet.size() > 0) {
 279                                         taxonDescription = descriptionSet.iterator().next();
 280                                 } else {
 281                                         taxonDescription = TaxonDescription.NewInstance();
 282                                         taxon.addDescription(taxonDescription);
 283                                 }
 284
 285                                 taxonUuid = taxonBase.getUuid();
 286                                 fauEuHelperTaxon= fauEuTaxonMap.get(taxonUuid);
 287
 288                                 for (FaunaEuropaeaDistribution fauEuHelperDistribution : fauEuHelperTaxon.getDistributions()) {
 289                                         namedArea = null;
 290                                         newDistribution = null;
 291                                         presenceAbsenceStatus = null;
 292
 293                                         if (fauEuHelperDistribution.getOccurrenceStatusId() != 0 && fauEuHelperDistribution.getOccurrenceStatusId() != 2 && fauEuHelperDistribution.getOccurrenceStatusId() != 1){
 294                                                 presenceAbsenceStatus = (PresenceAbsenceTermBase)getTermService().find(noData);
 295                                         }else{
 296                                                 presenceAbsenceStatus
 297                                                 = FaunaEuropaeaTransformer.occStatus2PresenceAbsence(fauEuHelperDistribution.getOccurrenceStatusId());
 298                                         }
 299
 300
 301
 302                                         namedArea = FaunaEuropaeaTransformer.areaId2TdwgArea(fauEuHelperDistribution);
 303
 304                                         if (namedArea == null){
 305                                                 UUID areaUuid= FaunaEuropaeaTransformer.getUUIDByAreaAbbr(fauEuHelperDistribution.getAreaCode());
 306                                                 namedArea = getNamedArea(state, areaUuid, fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaName(), fauEuHelperDistribution.getAreaCode(), null, null);
 307
 308                                         }
 309
 310                                         newDistribution = Distribution.NewInstance(namedArea, presenceAbsenceStatus);
 311                                         taxonDescription.addElement(newDistribution);
 312                                 }
 313                         }
 314                 }
 315                 return taxonList;
 316         }
 317
 318
 319         /* (non-Javadoc)
 320          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 321          */
 322         protected boolean isIgnore(FaunaEuropaeaImportState state){
 323                 return !state.getConfig().isDoOccurrence();
 324         }
 325 }