app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSpecimenImport.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.algaterra;
  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.Map;
  17 import java.util.Set;
  18 import java.util.UUID;
  19
  20 import org.apache.commons.lang.StringUtils;
  21 import org.apache.log4j.Logger;
  22 import org.springframework.stereotype.Component;
  23
  24 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  25 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade.DerivedUnitType;
  26 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  27 import eu.etaxonomy.cdm.io.algaterra.validation.AlgaTerraSpecimenImportValidator;
  28 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator;
  29 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState;
  30 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelTaxonImport;
  31 import eu.etaxonomy.cdm.io.common.IOValidator;
  32 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  33 import eu.etaxonomy.cdm.model.common.CdmBase;
  34 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.Marker;
  37 import eu.etaxonomy.cdm.model.common.MarkerType;
  38 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  39 import eu.etaxonomy.cdm.model.description.CategoricalData;
  40 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  41 import eu.etaxonomy.cdm.model.description.Feature;
  42 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  43 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  44 import eu.etaxonomy.cdm.model.description.Modifier;
  45 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  46 import eu.etaxonomy.cdm.model.description.State;
  47 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  48 import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
  49 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  50 import eu.etaxonomy.cdm.model.description.TextData;
  51 import eu.etaxonomy.cdm.model.name.BotanicalName;
  52 import eu.etaxonomy.cdm.model.name.Rank;
  53 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  54 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  55 import eu.etaxonomy.cdm.model.reference.Reference;
  56 import eu.etaxonomy.cdm.model.taxon.Taxon;
  57 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  58
  59
  60 /**
  61  * @author a.mueller
  62  * @created 01.09.2012
  63  */
  64 @Component
  65 public class AlgaTerraSpecimenImport  extends AlgaTerraSpecimenImportBase {
  66         private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImport.class);
  67
  68
  69         private static int modCount = 5000;
  70         private static final String pluralString = "specimen and observation";
  71         private static final String dbTableName = "Fact";  //??
  72
  73
  74         public AlgaTerraSpecimenImport(){
  75                 super();
  76         }
  77
  78
  79
  80         /* (non-Javadoc)
  81          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getIdQuery()
  82          */
  83         @Override
  84         protected String getIdQuery(BerlinModelImportState state) {
  85                 String result = " SELECT factId " +
  86                                 " FROM Fact " +
  87                                         " INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +
  88                                         "INNER JOIN PTaxon ON Fact.PTNameFk = PTaxon.PTNameFk AND Fact.PTRefFk = PTaxon.PTRefFk "
  89                                 + " WHERE FactCategoryFk = 202 "
  90                                 + " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId ";
  91                 return result;
  92         }
  93
  94         /* (non-Javadoc)
  95          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getRecordQuery(eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportConfigurator)
  96          */
  97         @Override
  98         protected String getRecordQuery(BerlinModelImportConfigurator config) {
  99                         String strQuery =
 100             " SELECT PTaxon.RIdentifier as taxonId, Fact.FactId, Fact.RecordBasis, EcoFact.*, " +
 101                " tg.ID AS GazetteerId, tg.L2Code, tg.L3Code, tg.L4Code, tg.Country, tg.ISOCountry, " +
 102                " ec.UUID as climateUuid, eh.UUID as habitatUuid, elf.UUID as lifeFormUuid" +
 103             " FROM Fact " +
 104                  " INNER JOIN EcoFact ON Fact.ExtensionFk = EcoFact.EcoFactId " +
 105                  " INNER JOIN PTaxon ON dbo.Fact.PTNameFk = dbo.PTaxon.PTNameFk AND dbo.Fact.PTRefFk = dbo.PTaxon.PTRefFk " +
 106                  " LEFT OUTER JOIN TDWGGazetteer tg ON EcoFact.TDWGGazetteerFk = tg.ID " +
 107                  " LEFT OUTER JOIN EcoClimate  ec  ON EcoFact.ClimateFk  = ec.ClimateId " +
 108                  " LEFT OUTER JOIN EcoHabitat  eh  ON EcoFact.HabitatFk  = eh.HabitatId " +
 109                  " LEFT OUTER JOIN EcoLifeForm elf ON EcoFact.LifeFormFk = elf.LifeFormId " +
 110               " WHERE Fact.FactCategoryFk = 202 AND (Fact.FactId IN (" + ID_LIST_TOKEN + ")  )"
 111             + " ORDER BY EcoFact.EcoFactId, PTaxon.RIdentifier, Fact.FactId "
 112             ;
 113                 return strQuery;
 114         }
 115
 116         /* (non-Javadoc)
 117          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#doPartition(eu.etaxonomy.cdm.io.berlinModel.in.ResultSetPartitioner, eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportState)
 118          */
 119         public boolean doPartition(ResultSetPartitioner partitioner, BerlinModelImportState bmState) {
 120                 boolean success = true;
 121
 122                 AlgaTerraImportState state = (AlgaTerraImportState)bmState;
 123                 try {
 124                         makeVocabulariesAndFeatures(state);
 125                 } catch (SQLException e1) {
 126                         logger.warn("Exception occurred when trying to create Ecofact vocabularies: " + e1.getMessage());
 127                         e1.printStackTrace();
 128                 }
 129                 Set<TaxonBase> taxaToSave = new HashSet<TaxonBase>();
 130
 131                 Map<String, TaxonBase> taxonMap = (Map<String, TaxonBase>) partitioner.getObjectMap(BerlinModelTaxonImport.NAMESPACE);
 132                 Map<String, DerivedUnit> ecoFactMap = (Map<String, DerivedUnit>) partitioner.getObjectMap(ECO_FACT_NAMESPACE);
 133
 134                 ResultSet rs = partitioner.getResultSet();
 135
 136                 try {
 137
 138                         int i = 0;
 139
 140                         //for each reference
 141             while (rs.next()){
 142
 143                         if ((i++ % modCount) == 0 && i!= 1 ){ logger.info("Specimen facts handled: " + (i-1));}
 144
 145                                 int newTaxonId = rs.getInt("taxonId");
 146                                 int factId = rs.getInt("FactId");
 147                                 int ecoFactId = rs.getInt("EcoFactId");
 148                                 String recordBasis = rs.getString("RecordBasis");
 149
 150                                 try {
 151
 152                                         //source ref
 153                                         Reference<?> sourceRef = state.getTransactionalSourceReference();
 154
 155                                         //facade
 156                                         DerivedUnitType type = makeDerivedUnitType(recordBasis);
 157                                         DerivedUnitFacade facade = getDerivedUnit(state, ecoFactId, ecoFactMap, type);
 158
 159                                         //field observation
 160                                         handleSingleSpecimen(rs, facade, state);
 161
 162                                         handleEcoFactSpecificSpecimen(rs,facade, state);
 163
 164                                         state.setCurrentFieldObservationNotNew(false);
 165
 166                                         //description element
 167                                         TaxonDescription taxonDescription = getTaxonDescription(state, newTaxonId, taxonMap, factId, sourceRef);
 168                                         IndividualsAssociation indAssociation = IndividualsAssociation.NewInstance();
 169                                         Feature feature = makeFeature(type);
 170                                         indAssociation.setAssociatedSpecimenOrObservation(facade.innerDerivedUnit());
 171                                         indAssociation.setFeature(feature);
 172                                         taxonDescription.addElement(indAssociation);
 173
 174                                         taxaToSave.add(taxonDescription.getTaxon());
 175
 176
 177                                 } catch (Exception e) {
 178                                         logger.warn("Exception in ecoFact: FactId " + factId + ". " + e.getMessage());
 179 //                                      e.printStackTrace();
 180                                 }
 181
 182             }
 183
 184 //            logger.warn("Specimen: " + countSpecimen + ", Descriptions: " + countDescriptions );
 185
 186                         logger.warn("Taxa to save: " + taxaToSave.size());
 187                         getTaxonService().save(taxaToSave);
 188
 189                         return success;
 190                 } catch (SQLException e) {
 191                         logger.error("SQLException:" +  e);
 192                         return false;
 193                 }
 194         }
 195
 196
 197
 198         private void handleEcoFactSpecificSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state) throws SQLException {
 199
 200                 Object alkalinityFlag = rs.getBoolean("AlkalinityFlag");
 201
 202                 //alkalinity marker
 203                 if (alkalinityFlag != null){
 204                         MarkerType alkalinityMarkerType = getMarkerType(state, uuidMarkerAlkalinity, "Alkalinity", "Alkalinity", null);
 205                         boolean alkFlag = Boolean.valueOf(alkalinityFlag.toString());
 206                         Marker alkalinityMarker = Marker.NewInstance(alkalinityMarkerType, alkFlag);
 207                         facade.getFieldObservation(true).addMarker(alkalinityMarker);
 208                 }
 209
 210
 211                 DescriptionBase<?> fieldDescription = getFieldObservationDescription(facade);
 212
 213                 //habitat, ecology, community, etc.
 214                 String habitat = rs.getString("HabitatExplanation");
 215
 216                 if (isNotBlank(habitat)){
 217                         Feature habitatExplanation = getFeature(state, uuidFeatureHabitatExplanation, "Habitat Explanation", "HabitatExplanation", null, null);
 218                         TextData textData = TextData.NewInstance(habitatExplanation);
 219                         textData.putText(Language.DEFAULT(), habitat);
 220                         fieldDescription.addElement(textData);
 221                 }
 222
 223                 String community = rs.getString("Comunity");
 224                 if (isNotBlank(community)){
 225                         Feature communityFeature = getFeature(state, uuidFeatureSpecimenCommunity, "Community", "The community of a specimen (e.g. other algae in the same sample)", null, null);
 226                         TextData textData = TextData.NewInstance(communityFeature);
 227                         textData.putText(Language.DEFAULT(), community);
 228                         fieldDescription.addElement(textData);
 229                 }
 230
 231                 String additionalData = rs.getString("AdditionalData");
 232                 if (isNotBlank(additionalData)){  //or handle it as Annotation ??
 233                         Feature additionalDataFeature = getFeature(state, uuidFeatureAdditionalData, "Additional Data", "Additional Data", null, null);
 234                         TextData textData = TextData.NewInstance(additionalDataFeature);
 235                         textData.putText(Language.DEFAULT(), additionalData);
 236                         fieldDescription.addElement(textData);
 237                 }
 238
 239                 String climateUuid = rs.getString("climateUuid");
 240                 String habitatUuid = rs.getString("habitatUuid");
 241                 String lifeFormUuid = rs.getString("lifeFormUuid");
 242
 243                 addCategoricalValue(state, fieldDescription, climateUuid, uuidFeatureAlgaTerraClimate);
 244                 addCategoricalValue(state, fieldDescription, habitatUuid, Feature.HABITAT().getUuid());
 245                 addCategoricalValue(state, fieldDescription, lifeFormUuid, uuidFeatureAlgaTerraLifeForm);
 246
 247
 248                 //collection
 249                 String voucher = rs.getString("Voucher");
 250                 if (StringUtils.isNotBlank(voucher)){
 251                         facade.setAccessionNumber(voucher);
 252                 }
 253
 254                 //parameters
 255                 makeParameter(state, rs, getFieldObservationDescription(facade));
 256
 257         }
 258
 259
 260
 261
 262         private void addCategoricalValue(AlgaTerraImportState importState, DescriptionBase description, String uuidTerm, UUID featureUuid) {
 263                 if (uuidTerm != null){
 264                         State state = this.getStateTerm(importState, UUID.fromString(uuidTerm));
 265                         Feature feature = getFeature(importState, featureUuid);
 266                         CategoricalData categoricalData = CategoricalData.NewInstance(state, feature);
 267                         description.addElement(categoricalData);
 268                 }
 269         }
 270
 271         private void makeParameter(AlgaTerraImportState state, ResultSet rs, DescriptionBase<?> descriptionBase) throws SQLException {
 272                 for (int i = 1; i <= 10; i++){
 273                         String valueStr = rs.getString(String.format("P%dValue", i));
 274                         String unitStr = rs.getString(String.format("P%dUnit", i));
 275                         String parameter = rs.getString(String.format("P%dParameter", i));
 276                         String method = rs.getString(String.format("P%dMethod", i));
 277
 278                         //method
 279                         if (StringUtils.isNotBlank(method)){
 280                                 logger.warn("Methods not yet handled: " + method);
 281                         }
 282                         //parameter
 283                         TermVocabulary<Feature> vocParameter = getVocabulary(uuidVocParameter, "Feature vocabulary for AlgaTerra measurement parameters", "Parameters", null, null, false, Feature.COMMON_NAME());
 284                         if (StringUtils.isNotBlank(parameter)){
 285                                 UUID featureUuid = getParameterFeatureUuid(state, parameter);
 286                                 Feature feature = getFeature(state, featureUuid, parameter, parameter, null, vocParameter);
 287                                 QuantitativeData quantData = QuantitativeData.NewInstance(feature);
 288
 289                                 //unit
 290                                 MeasurementUnit unit = getMeasurementUnit(state, unitStr);
 291                                 quantData.setUnit(unit);
 292                                 try {
 293
 294                                         Set<Modifier> valueModifier = new HashSet<Modifier>();
 295                                         valueStr = normalizeAndModifyValue(state, valueStr, valueModifier);
 296                                         //value
 297                                         Float valueFlt = Float.valueOf(valueStr);  //TODO maybe change model to Double ??
 298
 299                                         StatisticalMeasure measureSingleValue = getStatisticalMeasure(state, uuidStatMeasureSingleValue, "Value", "Single measurement value", null, null);
 300                                         StatisticalMeasurementValue value = StatisticalMeasurementValue.NewInstance(measureSingleValue, valueFlt);
 301                                         quantData.addStatisticalValue(value);
 302                                         descriptionBase.addElement(quantData);
 303
 304                                 } catch (NumberFormatException e) {
 305                                         logger.warn(String.format("Value '%s' can't be converted to double. Parameter %s not imported.", valueStr, parameter));
 306                                 }
 307                         }else if (isNotBlank(valueStr) || isNotBlank(unitStr) ){
 308                                 logger.warn("There is value or unit without parameter: " + i);
 309                         }
 310
 311
 312                 }
 313
 314         }
 315
 316         private String normalizeAndModifyValue(AlgaTerraImportState state, String valueStr, Set<Modifier> valueModifier) {
 317                 valueStr = valueStr.replace(",", ".");
 318                 if (valueStr.startsWith("<")){
 319                         TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance());
 320                         Modifier modifier = getModifier(state, uuidModifierLowerThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);
 321                         valueModifier.add(modifier);
 322                         valueStr = valueStr.replace("<", "");
 323                 }
 324                 if (valueStr.startsWith(">")){
 325                         TermVocabulary<Modifier> measurementValueModifierVocabulary = getVocabulary(uuidMeasurementValueModifier, "Measurement value modifier", "Measurement value modifier", null, null, false, Modifier.NewInstance());
 326                         Modifier modifier = getModifier(state, uuidModifierGreaterThan, "Lower", "Lower than the given measurement value", "<", measurementValueModifierVocabulary);
 327                         valueModifier.add(modifier);
 328                         valueStr = valueStr.replace(">", "");
 329                 }
 330                 return valueStr;
 331         }
 332
 333
 334
 335         private UUID getParameterFeatureUuid(AlgaTerraImportState state, String key) {
 336                 //TODO define some UUIDs in Transformer
 337                 UUID uuid = state.getParameterFeatureUuid(key);
 338                 if (uuid == null){
 339                         uuid = UUID.randomUUID();
 340                         state.putParameterFeatureUuid(key, uuid);
 341                 }
 342                 return uuid;
 343         }
 344
 345
 346
 347         /**
 348          * TODO move to InputTransformerBase
 349          * @param state
 350          * @param unitStr
 351          * @return
 352          */
 353         private MeasurementUnit getMeasurementUnit(AlgaTerraImportState state, String unitStr) {
 354                 if (StringUtils.isNotBlank(unitStr)){
 355                         UUID uuidMeasurementUnitMgL = UUID.fromString("7ac302c5-3cbd-4334-964a-bf5d11eb9ead");
 356                         UUID uuidMeasurementUnitMolMol = UUID.fromString("96b78d78-3e49-448f-8100-e7779b71dd53");
 357                         UUID uuidMeasurementUnitMicroMolSiL = UUID.fromString("2cb8bc85-a4af-42f1-b80b-34c36c9f75d4");
 358                         UUID uuidMeasurementUnitMicroMolL = UUID.fromString("a631f62e-377e-405c-bd1a-76885b13a72b");
 359                         UUID uuidMeasurementUnitDegreeC = UUID.fromString("55222aec-d5be-413e-8db7-d9a48c316c6c");
 360                         UUID uuidMeasurementUnitPercent = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f");
 361                         UUID uuidMeasurementUnitCm = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f");
 362                         UUID uuidMeasurementUnitMicroSiCm = UUID.fromString("3ea3110e-f048-4bed-8bfe-33c60f63626f");
 363
 364
 365                         if (unitStr.equalsIgnoreCase("mg/L")){
 366                                 return getMeasurementUnit(state, uuidMeasurementUnitMgL, unitStr, unitStr, unitStr, null);
 367                         }else if (unitStr.equalsIgnoreCase("mol/mol")){
 368                                 return getMeasurementUnit(state, uuidMeasurementUnitMolMol, unitStr, unitStr, unitStr, null);
 369                         }else if (unitStr.equalsIgnoreCase("\u00B5mol Si/L")){   //µmol Si/L
 370                                 return getMeasurementUnit(state, uuidMeasurementUnitMicroMolSiL, unitStr, unitStr, unitStr, null);
 371                         }else if (unitStr.equalsIgnoreCase("\u00B5mol/L")){             //µmol/L
 372                                 return getMeasurementUnit(state, uuidMeasurementUnitMicroMolL, unitStr, unitStr, unitStr, null);
 373                         }else if (unitStr.equalsIgnoreCase("\u00B0C")){               //°C
 374                                 return getMeasurementUnit(state, uuidMeasurementUnitDegreeC, unitStr, unitStr, unitStr, null);
 375                         }else if (unitStr.equalsIgnoreCase("%")){
 376                                 return getMeasurementUnit(state, uuidMeasurementUnitPercent, unitStr, unitStr, unitStr, null);
 377                         }else if (unitStr.equalsIgnoreCase("cm")){
 378                                 return getMeasurementUnit(state, uuidMeasurementUnitCm, unitStr, unitStr, unitStr, null);
 379                         }else if (unitStr.equalsIgnoreCase("\u00B5S/cm")){   //µS/cm
 380                                 return getMeasurementUnit(state, uuidMeasurementUnitMicroSiCm, unitStr, unitStr, unitStr, null);
 381                         }else{
 382                                 logger.warn("MeasurementUnit was not recognized");
 383                                 return null;
 384                         }
 385                 }else{
 386                         return null;
 387                 }
 388         }
 389
 390
 391
 392
 393
 394         /**
 395          * @param state
 396          * @param ecoFactId
 397          * @param derivedUnitMap
 398          * @param type
 399          * @return
 400          */
 401         private DerivedUnitFacade getDerivedUnit(AlgaTerraImportState state, int ecoFactId, Map<String, DerivedUnit> derivedUnitMap, DerivedUnitType type) {
 402                 String key = String.valueOf(ecoFactId);
 403                 DerivedUnit derivedUnit = derivedUnitMap.get(key);
 404                 DerivedUnitFacade facade;
 405                 if (derivedUnit == null){
 406                         facade = DerivedUnitFacade.NewInstance(type);
 407                         derivedUnitMap.put(key, derivedUnit);
 408                 }else{
 409                         try {
 410                                 facade = DerivedUnitFacade.NewInstance(derivedUnit);
 411                         } catch (DerivedUnitFacadeNotSupportedException e) {
 412                                 logger.error(e.getMessage());
 413                                 facade = DerivedUnitFacade.NewInstance(type);
 414                         }
 415                 }
 416
 417                 return facade;
 418         }
 419
 420         private Feature makeFeature(DerivedUnitType type) {
 421                 if (type.equals(DerivedUnitType.DerivedUnit)){
 422                         return Feature.INDIVIDUALS_ASSOCIATION();
 423                 }else if (type.equals(DerivedUnitType.FieldObservation) || type.equals(DerivedUnitType.Observation) ){
 424                         return Feature.OBSERVATION();
 425                 }else if (type.equals(DerivedUnitType.Fossil) || type.equals(DerivedUnitType.LivingBeing) || type.equals(DerivedUnitType.Specimen )){
 426                         return Feature.SPECIMEN();
 427                 }
 428                 logger.warn("No feature defined for derived unit type: " + type);
 429                 return null;
 430         }
 431
 432
 433         private DerivedUnitType makeDerivedUnitType(String recordBasis) {
 434                 DerivedUnitType result = null;
 435                 if (StringUtils.isBlank(recordBasis)){
 436                         result = DerivedUnitType.DerivedUnit;
 437                 } else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){
 438                         result = DerivedUnitType.Fossil;
 439                 }else if (recordBasis.equalsIgnoreCase("HumanObservation")){
 440                         result = DerivedUnitType.Observation;
 441                 }else if (recordBasis.equalsIgnoreCase("Literature")){
 442                         logger.warn("Literature record basis not yet supported");
 443                         result = DerivedUnitType.DerivedUnit;
 444                 }else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){
 445                         result = DerivedUnitType.LivingBeing;
 446                 }else if (recordBasis.equalsIgnoreCase("MachineObservation")){
 447                         logger.warn("MachineObservation record basis not yet supported");
 448                         result = DerivedUnitType.Observation;
 449                 }else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){
 450                         result = DerivedUnitType.Specimen;
 451                 }
 452                 return result;
 453         }
 454
 455         /* (non-Javadoc)
 456          * @see eu.etaxonomy.cdm.io.berlinModel.in.IPartitionedIO#getRelatedObjectsForPartition(java.sql.ResultSet)
 457          */
 458         public Map<Object, Map<String, ? extends CdmBase>> getRelatedObjectsForPartition(ResultSet rs) {
 459                 String nameSpace;
 460                 Class cdmClass;
 461                 Set<String> idSet;
 462                 Map<Object, Map<String, ? extends CdmBase>> result = new HashMap<Object, Map<String, ? extends CdmBase>>();
 463
 464                 try{
 465                         Set<String> taxonIdSet = new HashSet<String>();
 466                         Set<String> fieldObservationIdSet = new HashSet<String>();
 467                         Set<String> termsIdSet = new HashSet<String>();
 468
 469                         while (rs.next()){
 470                                 handleForeignKey(rs, taxonIdSet, "taxonId");
 471                                 handleForeignKey(rs, fieldObservationIdSet, "ecoFactId");
 472                                 handleForeignKey(rs, termsIdSet, "ClimateFk");
 473                                 handleForeignKey(rs, termsIdSet, "HabitatFk");
 474                                 handleForeignKey(rs, termsIdSet, "LifeFormFk");
 475                         }
 476
 477                         //taxon map
 478                         nameSpace = BerlinModelTaxonImport.NAMESPACE;
 479                         cdmClass = TaxonBase.class;
 480                         idSet = taxonIdSet;
 481                         Map<String, TaxonBase> objectMap = (Map<String, TaxonBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 482                         result.put(nameSpace, objectMap);
 483
 484                         //field observation map map
 485                         nameSpace = AlgaTerraSpecimenImport.ECO_FACT_NAMESPACE;
 486                         cdmClass = FieldObservation.class;
 487                         idSet = fieldObservationIdSet;
 488                         Map<String, FieldObservation> fieldObservationMap = (Map<String, FieldObservation>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 489                         result.put(nameSpace, fieldObservationMap);
 490
 491                         //terms
 492                         nameSpace = AlgaTerraSpecimenImport.TERMS_NAMESPACE;
 493                         cdmClass = FieldObservation.class;
 494                         idSet = termsIdSet;
 495                         Map<String, DefinedTermBase> termMap = (Map<String, DefinedTermBase>)getCommonService().getSourcedObjectsByIdInSource(cdmClass, idSet, nameSpace);
 496                         result.put(nameSpace, termMap);
 497
 498                 } catch (SQLException e) {
 499                         throw new RuntimeException(e);
 500                 }
 501                 return result;
 502         }
 503
 504
 505         /**
 506          * Use same TaxonDescription if two records belong to the same taxon
 507          * @param state
 508          * @param newTaxonId
 509          * @param oldTaxonId
 510          * @param oldDescription
 511          * @param taxonMap
 512          * @return
 513          */
 514         private TaxonDescription getTaxonDescription(AlgaTerraImportState state, int newTaxonId, Map<String, TaxonBase> taxonMap, int factId, Reference<?> sourceSec){
 515                 TaxonDescription result = null;
 516                 TaxonBase<?> taxonBase = taxonMap.get(String.valueOf(newTaxonId));
 517
 518                 //TODO for testing
 519                 if (taxonBase == null && ! state.getConfig().isDoTaxa()){
 520                         taxonBase = Taxon.NewInstance(BotanicalName.NewInstance(Rank.SPECIES()), null);
 521                 }
 522
 523                 Taxon taxon;
 524                 if ( taxonBase instanceof Taxon ) {
 525                         taxon = (Taxon) taxonBase;
 526                 } else if (taxonBase != null) {
 527                         logger.warn("TaxonBase for Fact(Specimen) with factId" + factId + " was not of type Taxon but: " + taxonBase.getClass().getSimpleName());
 528                         return null;
 529                 } else {
 530                         logger.warn("TaxonBase for Fact(Specimen) " + factId + " is null.");
 531                         return null;
 532                 }
 533                 Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
 534                 if (descriptionSet.size() > 0) {
 535                         result = descriptionSet.iterator().next();
 536                 }else{
 537                         result = TaxonDescription.NewInstance();
 538                         result.setTitleCache(sourceSec.getTitleCache(), true);
 539                         taxon.addDescription(result);
 540                 }
 541                 return result;
 542         }
 543
 544
 545         /* (non-Javadoc)
 546          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#doCheck(eu.etaxonomy.cdm.io.common.IoStateBase)
 547          */
 548         @Override
 549         protected boolean doCheck(BerlinModelImportState state){
 550                 IOValidator<BerlinModelImportState> validator = new AlgaTerraSpecimenImportValidator();
 551                 return validator.validate(state);
 552         }
 553
 554         /* (non-Javadoc)
 555          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getTableName()
 556          */
 557         @Override
 558         protected String getTableName() {
 559                 return dbTableName;
 560         }
 561
 562         /* (non-Javadoc)
 563          * @see eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase#getPluralString()
 564          */
 565         @Override
 566         public String getPluralString() {
 567                 return pluralString;
 568         }
 569
 570         /* (non-Javadoc)
 571          * @see eu.etaxonomy.cdm.io.common.CdmIoBase#isIgnore(eu.etaxonomy.cdm.io.common.IImportConfigurator)
 572          */
 573         protected boolean isIgnore(BerlinModelImportState state){
 574                 return ! ((AlgaTerraImportState)state).getAlgaTerraConfigurator().isDoSpecimen();
 575         }
 576
 577 }