app-import/src/main/java/eu/etaxonomy/cdm/io/algaterra/AlgaTerraSpecimenImportBase.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.net.URI;
  13 import java.sql.Date;
  14 import java.sql.ResultSet;
  15 import java.sql.SQLException;
  16 import java.util.HashMap;
  17 import java.util.Map;
  18 import java.util.Set;
  19 import java.util.UUID;
  20
  21 import org.apache.commons.lang.StringUtils;
  22 import org.apache.log4j.Logger;
  23 import org.springframework.transaction.TransactionStatus;
  24
  25 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  26 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;
  27 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  28 import eu.etaxonomy.cdm.io.common.Source;
  29 import eu.etaxonomy.cdm.io.common.TdwgAreaProvider;
  30 import eu.etaxonomy.cdm.model.agent.Team;
  31 import eu.etaxonomy.cdm.model.agent.TeamOrPersonBase;
  32 import eu.etaxonomy.cdm.model.common.Annotation;
  33 import eu.etaxonomy.cdm.model.common.AnnotationType;
  34 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  37 import eu.etaxonomy.cdm.model.common.TermType;
  38 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  39 import eu.etaxonomy.cdm.model.common.TimePeriod;
  40 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  41 import eu.etaxonomy.cdm.model.description.Feature;
  42 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  43 import eu.etaxonomy.cdm.model.description.State;
  44 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  45 import eu.etaxonomy.cdm.model.location.Country;
  46 import eu.etaxonomy.cdm.model.location.NamedArea;
  47 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  48 import eu.etaxonomy.cdm.model.location.Point;
  49 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  50 import eu.etaxonomy.cdm.model.occurrence.Collection;
  51 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
  52 import eu.etaxonomy.cdm.model.reference.Reference;
  53 import eu.etaxonomy.cdm.model.taxon.Taxon;
  54
  55 /**
  56  * @author a.mueller
  57  * @created 12.09.2012
  58  */
  59 public abstract class AlgaTerraSpecimenImportBase extends BerlinModelImportBase{
  60         private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImportBase.class);
  61
  62         public static final String ECO_FACT_FIELD_OBSERVATION_NAMESPACE = "EcoFact_FieldObservation";
  63         public static final String ECO_FACT_DERIVED_UNIT_NAMESPACE = "EcoFact_DerivedUnit";
  64         public static final String TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE = "TypeSpecimen_FieldObservation";
  65         public static final String TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE = "TypeSpecimen_DerivedUnit";
  66         public static final String FACT_ECOLOGY_NAMESPACE = "Fact (Ecology)";
  67
  68
  69         public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";
  70
  71         //TODO move to transformrer
  72         final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594");
  73         final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94");
  74         public final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");
  75         public final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");
  76         public final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f");
  77
  78         final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");
  79         final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");
  80         final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");
  81
  82         public final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");
  83         public final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");
  84         public final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");
  85
  86         final static UUID uuidVocParameter = UUID.fromString("45888b40-5bbb-4293-aa1e-02479796cd7c");
  87         final static UUID uuidStatMeasureSingleValue = UUID.fromString("eb4c3d98-4d4b-4c37-8eb4-17315ce79920");
  88         final static UUID uuidMeasurementValueModifier = UUID.fromString("0218a7a3-f6c0-4d06-a4f8-6b50b73aef5e");
  89
  90         final static UUID uuidModifierLowerThan = UUID.fromString("2b500085-6bef-4003-b6ea-e0ad0237d79d");
  91         final static UUID uuidModifierGreaterThan = UUID.fromString("828df49d-c745-48f7-b083-0ada43356c34");
  92
  93         public AlgaTerraSpecimenImportBase(String tableName, String pluralString) {
  94                 super(tableName, pluralString);
  95         }
  96
  97         /**
  98          * Creates the vocabularies and the features for Climate, Habitat and Lifeform
  99          * @param state
 100          * @throws SQLException
 101          */
 102         protected void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {
 103                 String abbrevLabel = null;
 104                 URI uri = null;
 105
 106                 if (! state.isSpecimenVocabulariesCreated()){
 107
 108                         TransactionStatus txStatus = this.startTransaction();
 109
 110                         boolean isOrdered = true;
 111                         State tmp = State.NewInstance();
 112                         OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary<State>)getVocabulary(TermType.State, uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, tmp);
 113                         OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary<State>)getVocabulary(TermType.State, uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, tmp);
 114                         OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary<State>)getVocabulary(TermType.State, uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, tmp);
 115
 116                         Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);
 117                         feature.setSupportsCategoricalData(true);
 118
 119                         feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);
 120                         feature.setSupportsCategoricalData(true);
 121
 122                         feature = Feature.HABITAT();
 123                         feature.setSupportsCategoricalData(true);
 124                         getTermService().saveOrUpdate(feature);
 125
 126                         Source source = state.getAlgaTerraConfigurator().getSource();
 127
 128                         String climateSql = "SELECT * FROM EcoClimate";
 129                         ResultSet rs = source.getResultSet(climateSql);
 130                         while (rs.next()){
 131                                 String climate = rs.getString("Climate");
 132                                 String description = rs.getString("Description");
 133                                 Integer id = rs.getInt("ClimateId");
 134                                 UUID uuid = UUID.fromString(rs.getString("UUID"));
 135                                 State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);
 136                                 addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getTransactionalSourceReference());
 137                                 getTermService().saveOrUpdate(stateTerm);
 138                         }
 139
 140                         String habitatSql = "SELECT * FROM EcoHabitat";
 141                         rs = source.getResultSet(habitatSql);
 142                         while (rs.next()){
 143                                 String habitat = rs.getString("Habitat");
 144                                 String description = rs.getString("Description");
 145                                 Integer id = rs.getInt("HabitatId");
 146                                 UUID uuid = UUID.fromString(rs.getString("UUID"));
 147                                 State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);
 148                                 addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getTransactionalSourceReference());
 149                                 getTermService().saveOrUpdate(stateTerm);
 150                         }
 151
 152                         String lifeformSql = "SELECT * FROM EcoLifeForm";
 153                         rs = source.getResultSet(lifeformSql);
 154                         while (rs.next()){
 155                                 String lifeform = rs.getString("LifeForm");
 156                                 String description = rs.getString("Description");
 157                                 Integer id = rs.getInt("LifeFormId");
 158                                 UUID uuid = UUID.fromString(rs.getString("UUID"));
 159                                 State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);
 160                                 addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getTransactionalSourceReference());
 161                                 getTermService().saveOrUpdate(stateTerm);
 162                         }
 163
 164                         //material category
 165                         TermVocabulary<DefinedTerm> materialCategoryVoc = getVocabulary(TermType.KindOfUnit, AlgaTerraImportTransformer.uuidKindOfUnitVoc, "Alga Terra Material Category", "Alga Terra Material Category", abbrevLabel, uri, false, DefinedTerm.NewKindOfUnitInstance(null, null, null));
 166                         getVocabularyService().save(materialCategoryVoc);
 167
 168                         String materialSql = "SELECT * FROM MaterialCategory WHERE MaterialCategoryId <> 16 ";
 169                         rs = source.getResultSet(materialSql);
 170                         while (rs.next()){
 171                                 Integer id = rs.getInt("MaterialCategoryId");
 172                                 String category = rs.getString("MaterialCategory");
 173                                 String description = rs.getString("Description");
 174                                 UUID uuid = UUID.randomUUID();
 175
 176                                 DefinedTerm kindOfUnit = DefinedTerm.NewKindOfUnitInstance(description, category, null);
 177                                 kindOfUnit.setUuid(uuid);
 178                                 addOriginalSource(kindOfUnit, id.toString(), "MaterialCategory", state.getTransactionalSourceReference());
 179                                 materialCategoryVoc.addTerm(kindOfUnit);
 180                                 getTermService().saveOrUpdate(kindOfUnit);
 181                                 materialCategoryMapping.put(id, uuid);
 182                         }
 183
 184                         //areas
 185                         OrderedTermVocabulary<NamedArea> informalAreasVoc = (OrderedTermVocabulary<NamedArea>)getVocabulary(TermType.NamedArea, AlgaTerraImportTransformer.uuidNamedAreaVocAlgaTerraInformalAreas, "AlgaTerra Specific Areas", "AlgaTerra Specific Areas", abbrevLabel, uri, true, NamedArea.NewInstance());
 186                         getVocabularyService().save(informalAreasVoc);
 187
 188                         String areaSql = "SELECT * FROM TDWGGazetteer WHERE subL4 = 1 ";
 189                         rs = source.getResultSet(areaSql);
 190                         while (rs.next()){
 191                                 String l1Code = rs.getString("L1Code");
 192                                 String l2Code = rs.getString("L2Code");
 193                                 String l3Code = rs.getString("L3Code");
 194                                 String l4Code = rs.getString("L4Code");
 195                                 String gazetteer = rs.getString("Gazetteer");
 196                                 Integer id = rs.getInt("ID");
 197                                 String notes = rs.getString("Notes");
 198                                 //TODO stable uuids
 199 //                              UUID uuid = UUID.fromString(rs.getString("UUID"));
 200                                 UUID uuid = UUID.randomUUID();
 201                                 subL4Mapping.put(id, uuid);
 202
 203                                 String tdwgCode =  (l4Code != null) ? l4Code : (l3Code != null) ? l3Code : (l2Code != null) ? l2Code : l1Code;
 204
 205                                 NamedArea tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwgCode);
 206                                 NamedArea newArea  = getNamedArea(state, uuid ,gazetteer, gazetteer, null, null, null, informalAreasVoc, TermMatchMode.UUID_ONLY, null);
 207                                 if (isNotBlank(notes)){
 208                                         newArea.addAnnotation(Annotation.NewInstance(notes, AnnotationType.EDITORIAL(), Language.DEFAULT()));
 209                                 }
 210
 211                                 addOriginalSource(newArea, id.toString(), "TDWGGazetteer", state.getTransactionalSourceReference());
 212                                 getTermService().saveOrUpdate(newArea);
 213                                 newArea.setPartOf(tdwgArea);
 214                                 informalAreasVoc.addTerm(newArea);
 215                         }
 216
 217                         this.commitTransaction(txStatus);
 218
 219                         state.setSpecimenVocabulariesCreated(true);
 220                 }
 221         }
 222
 223         //tmp
 224         static Map<Integer, UUID> subL4Mapping = new HashMap<Integer, UUID>();
 225         static Map<Integer, UUID> materialCategoryMapping = new HashMap<Integer, UUID>();
 226
 227         protected String getLocalityString(){
 228                 return "Locality";
 229         }
 230
 231         protected void handleFieldObservationSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {
 232                 //FIXME missing fields #3084, #3085, #3080
 233                 try {
 234
 235                         Integer unitId = nullSafeInt(rs, "unitId");
 236                         String locality = rs.getString(getLocalityString());
 237                         Double latitude = nullSafeDouble(rs, "Latitude");
 238                         Double longitude = nullSafeDouble(rs, "Longitude");
 239                         Integer errorRadius = nullSafeInt(rs,"Prec");
 240                         String geoCodeMethod = rs.getString("GeoCodeMethod");
 241
 242                         Integer altitude = nullSafeInt(rs, "Altitude");
 243                         Integer lowerAltitude = nullSafeInt(rs, "AltitudeLowerValue");
 244                         String altitudeUnit = rs.getString("AltitudeUnit");
 245                         Double depth = nullSafeDouble(rs, "Depth");
 246                         Double depthLow = nullSafeDouble(rs, "DepthLow");
 247
 248                         String collectorsNumber = rs.getString("CollectorsNumber");
 249                         Date collectionDateStart = rs.getDate("CollectionDate");
 250                         Date collectionDateEnd = rs.getDate("CollectionDateEnd");
 251
 252                         //location
 253                         facade.setLocality(locality);
 254
 255                         //exact location
 256                         ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);
 257                         if (longitude != null || latitude != null || referenceSystem != null || errorRadius != null){
 258                                 Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);
 259                                 facade.setExactLocation(exactLocation);
 260                         }
 261
 262                         //altitude, depth
 263                         if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){
 264                                 logger.warn("Altitude unit is not [m] but: " +  altitudeUnit);
 265                         }
 266                         if ( altitude != null){
 267                                 if (lowerAltitude == null){
 268                                         facade.setAbsoluteElevation(altitude);
 269                                 }else{
 270                                         facade.setAbsoluteElevationRange(lowerAltitude,altitude);
 271                                 }
 272                         }
 273                         if ( depth != null){
 274                                 if (depthLow == null){
 275                                         facade.setDistanceToWaterSurface(depth);
 276                                 }else{
 277                                         //TODO which direction is correct?
 278                                         facade.setDistanceToWaterSurfaceRange(depth, depthLow);
 279                                 }
 280                         }
 281
 282                         //field
 283                         facade.setFieldNumber(collectorsNumber);
 284                         TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);
 285                         facade.setGatheringPeriod(gatheringPeriod);
 286                         handleCollectorTeam(state, facade, rs);
 287
 288                         //areas
 289                         makeAreas(state, rs, facade);
 290
 291                         //notes
 292                         //=> not required according to Henning
 293
 294                         //id, created, updated, notes
 295                         if (unitId != null){
 296                                 this.doIdCreatedUpdatedNotes(state, facade.innerFieldUnit(), rs, unitId, getFieldObservationNameSpace());
 297                         }else{
 298                                 logger.warn("FieldObservation has no unitId: " +  facade.innerFieldUnit() + ": " + getFieldObservationNameSpace());
 299                         }
 300                 } catch (Exception e) {
 301                         throw new RuntimeException(e);
 302                 }
 303
 304         }
 305
 306         protected void handleFirstDerivedSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {
 307                 Integer unitId = nullSafeInt(rs, "unitId");
 308                 Integer collectionFk = nullSafeInt(rs,"CollectionFk");
 309                 String label = rs.getString("Label");
 310
 311                 //collection
 312                 if (collectionFk != null){
 313                         Collection subCollection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION, String.valueOf(collectionFk), Collection.class);
 314                         if (subCollection != null){
 315                                 facade.setCollection(subCollection);
 316                         }else{
 317                                 Collection collection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_COLLECTION, String.valueOf(collectionFk), Collection.class);
 318                                 if (collection == null){
 319                                         logger.warn("Collection for collectionFK " + collectionFk + " can not be found.");
 320                                 }
 321                                 facade.setCollection(collection);
 322                         }
 323                 }
 324
 325                 //Label
 326                 if (isNotBlank(label)){
 327                         //TODO implement label #4218, #3090, #3084
 328                         logger.warn("Label not yet implemented for specimen, #4218, #3090, #3084");
 329                 }
 330
 331                 //TODO id, created for fact +  ecoFact
 332                 //      this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);
 333                 if (unitId != null){
 334                         this.doIdCreatedUpdatedNotes(state, facade.innerDerivedUnit(), rs, unitId, getDerivedUnitNameSpace());
 335                 }else{
 336                         logger.warn("Specimen has no unitId: " +  facade.innerDerivedUnit() + ": " + getDerivedUnitNameSpace());
 337                 }
 338         }
 339
 340
 341
 342         protected abstract String getDerivedUnitNameSpace();
 343
 344         protected abstract String getFieldObservationNameSpace();
 345
 346
 347         protected DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {
 348                 Set<DescriptionBase> descriptions = facade.innerFieldUnit().getDescriptions();
 349                 for (DescriptionBase desc : descriptions){
 350                         if (desc.isImageGallery() == false){
 351                                 return desc;
 352                         }
 353                 }
 354                 SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldUnit());
 355                 descriptions.add(specDesc);
 356                 return specDesc;
 357         }
 358
 359
 360         private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {
 361                 Integer gazetteerId = nullSafeInt(rs, "GazetteerId");
 362                 if (gazetteerId != null){
 363                         //TDWG
 364                         NamedArea tdwgArea;
 365                         String tdwg4 = rs.getString("L4Code");
 366                         if (isNotBlank(tdwg4)){
 367                                 tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwg4);
 368                         }else{
 369                                 String tdwg3 = rs.getString("L3Code");
 370                                 if (isNotBlank(tdwg3)){
 371                                         tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(tdwg3);
 372                                 }else{
 373                                         Number tdwg2D = nullSafeDouble(rs, "L2Code");
 374                                         if (tdwg2D != null){
 375                                                 Integer tdwg2 = tdwg2D.intValue();
 376                                                 tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));
 377                                         }else{
 378                                                 Number tdwg1D = nullSafeDouble(rs, "L1Code");
 379                                                 if (tdwg1D != null){
 380                                                         Integer tdwg1 = tdwg1D.intValue();
 381                                                         tdwgArea = TdwgAreaProvider.getAreaByTdwgAbbreviation(String.valueOf(tdwg1));
 382                                                 }else{
 383                                                         tdwgArea = null;
 384                                                 }
 385                                         }
 386                                 }
 387                         }
 388                         if (tdwgArea == null){
 389                                 logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);
 390                         }else{
 391                                 facade.addCollectingArea(tdwgArea);
 392                         }
 393
 394                         //Countries
 395                         Country country = null;
 396                         String isoCountry = rs.getString("ISOCountry");
 397                         String countryStr = rs.getString("Country");
 398                         if (isNotBlank(isoCountry)){
 399                                 country = Country.getCountryByIso3166A2(isoCountry);
 400                         }else if (isNotBlank(countryStr)){
 401                                 logger.warn("Country exists but no ISO code");
 402                         }else{
 403
 404                         }
 405
 406                         NamedArea subL4Area = null;
 407                         Boolean subL4 = nullSafeBoolean(rs, "subL4");
 408                         if (subL4 != null && subL4.booleanValue() == true){
 409                                 subL4Area = makeSubL4Area(state, gazetteerId);
 410                                 if (subL4Area != null){
 411                                         facade.addCollectingArea(subL4Area);
 412                                 }else{
 413                                         logger.warn("SubL4 area not found for gazetteerId: " + gazetteerId);
 414                                 }
 415                         }
 416
 417                         if (country == null ){
 418                                 if (! gazetteerId.equals(40)){//special handling for Borneo, TDWG area is enough here as it matches exactly
 419                                         if (subL4Area == null ){
 420                                                 logger.warn("Country does not exist and SubL4 could not be found for GazetteerID " + gazetteerId);
 421                                         }else {
 422                                                 logger.info("Country could not be defined but subL4 area was added");
 423                                         }
 424                                 }
 425                         }else{
 426                                 facade.setCountry(country);
 427                         }
 428
 429                 }
 430
 431                 //Waterbody
 432                 NamedArea waterbody = null;
 433                 String waterbodyStr = rs.getString("WaterBody");
 434                 if (isNotBlank(waterbodyStr)){
 435                         if (waterbodyStr.equals("Atlantic Ocean")){
 436                                 waterbody = NamedArea.ATLANTICOCEAN();
 437                         }else if (waterbodyStr.equals("Pacific Ocean")){
 438                                 waterbody = NamedArea.PACIFICOCEAN();
 439                         }else if (waterbodyStr.equals("Indian Ocean")){
 440                                 waterbody = NamedArea.INDIANOCEAN();
 441                         }else if (waterbodyStr.equals("Arctic Ocean")){
 442                                 waterbody = NamedArea.ARCTICOCEAN();
 443                         }else{
 444                                 logger.warn("Waterbody not recognized: " + waterbody);
 445                         }
 446                         if (waterbody != null){
 447                                 facade.addCollectingArea(waterbody);
 448                         }
 449                 }
 450
 451
 452                 //countries sub
 453                 //TODO -> SpecimenImport (not existing in TypeSpecimen)
 454         }
 455
 456
 457         private NamedArea makeSubL4Area(AlgaTerraImportState state, Integer gazetteerId) {
 458                 UUID uuid = subL4Mapping.get(gazetteerId);
 459                 NamedArea area = (NamedArea)getTermService().find(uuid);
 460                 if (area == null){
 461                         logger.warn("SubL4 area could not be found in repository");
 462                 }
 463                 return area;
 464         }
 465
 466         private boolean handleMissingCountry(AlgaTerraImportState state, DerivedUnitFacade facade, Integer gazetteerId) {
 467                 NamedArea area = null;
 468                 if (gazetteerId != null){
 469                         if (gazetteerId.equals(42)){
 470                                 area = getNamedArea(state, AlgaTerraImportTransformer.uuidNamedAreaBorneo, null, null, null, null, null);
 471                         }else if (gazetteerId.equals(1684)){
 472                                 area = getNamedArea(state, AlgaTerraImportTransformer.uuidNamedAreaPatagonia, null, null, null, null, null);
 473                         }else if (gazetteerId.equals(2167)){
 474                                 area = getNamedArea(state, AlgaTerraImportTransformer.uuidNamedAreaTierraDelFuego, null, null, null, null, null);
 475                         }
 476                 }
 477                 if (area != null){
 478                         facade.addCollectingArea(area);
 479                         return true;
 480                 }
 481                 return false;
 482
 483         }
 484
 485         protected SpecimenOrObservationType makeDerivedUnitType(String recordBasis) {
 486                 SpecimenOrObservationType result = null;
 487                 if (StringUtils.isBlank(recordBasis)){
 488                         result = SpecimenOrObservationType.DerivedUnit;
 489                 } else if (recordBasis.equalsIgnoreCase("FossileSpecimen")){
 490                         result = SpecimenOrObservationType.Fossil;
 491                 }else if (recordBasis.equalsIgnoreCase("HumanObservation")){
 492                         result = SpecimenOrObservationType.HumanObservation;
 493                 }else if (recordBasis.equalsIgnoreCase("Literature")){
 494                         //FIXME
 495                         logger.warn("Literature record basis not yet supported");
 496                         result = SpecimenOrObservationType.DerivedUnit;
 497                 }else if (recordBasis.equalsIgnoreCase("LivingSpecimen")){
 498                         result = SpecimenOrObservationType.LivingSpecimen;
 499                 }else if (recordBasis.equalsIgnoreCase("MachineObservation")){
 500                         result = SpecimenOrObservationType.MachineObservation;
 501                 }else if (recordBasis.equalsIgnoreCase("Observation")){
 502                         result = SpecimenOrObservationType.Observation;
 503                 }else if (recordBasis.equalsIgnoreCase("LivingCulture")){
 504                         //FIXME
 505                         logger.warn("LivingCulture record basis not yet supported");
 506                         result = SpecimenOrObservationType.DerivedUnit;
 507                 }else if (recordBasis.equalsIgnoreCase("PreservedSpecimen")){
 508                         result = SpecimenOrObservationType.PreservedSpecimen;
 509                 }
 510                 return result;
 511         }
 512
 513
 514         protected Feature makeFeature(SpecimenOrObservationType type, AlgaTerraImportState state) {
 515                 if (type.equals(SpecimenOrObservationType.DerivedUnit)){
 516                         return Feature.INDIVIDUALS_ASSOCIATION();
 517                 }else if (type.isFeatureObservation()){
 518                         return Feature.OBSERVATION();
 519                 }else if (type.isPreservedSpecimen()){
 520                         return Feature.SPECIMEN();
 521                 }else if (type.equals(SpecimenOrObservationType.LivingSpecimen)){
 522                         UUID uuid = AlgaTerraImportTransformer.uuidFeatureLivingSpecimen;
 523                         Feature feature = getFeature(state, uuid, "Living Specimen", "Living Specimen", null, Feature.SPECIMEN().getVocabulary());
 524                         if (feature == null){
 525                                 logger.warn("Living Specimen Feature could not be created");
 526                         }
 527                         return feature;
 528                 }
 529                 logger.warn("No feature defined for derived unit type: " + type);
 530                 return null;
 531         }
 532
 533         private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {
 534                 if (StringUtils.isBlank(geoCodeMethod)){
 535                         return null;
 536                 }else if(geoCodeMethod.startsWith("GPS")){
 537                         getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());
 538                         return ReferenceSystem.WGS84();
 539                 }else if(geoCodeMethod.startsWith("Google")){
 540                         return ReferenceSystem.GOOGLE_EARTH();
 541                 }else if(geoCodeMethod.startsWith("Map")){
 542                         return ReferenceSystem.MAP();
 543                 }else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){
 544                         return ReferenceSystem.WGS84();
 545                 }else {
 546                         logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");
 547                         return null;
 548                 }
 549         }
 550
 551
 552
 553
 554         private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {
 555                 String collector = rs.getString("Collector");
 556                 TeamOrPersonBase<?> author = getAuthor(collector);
 557                 facade.setCollector(author);
 558         }
 559
 560         /**
 561          * @param facade
 562          * @param collector
 563          */
 564         protected TeamOrPersonBase<?> getAuthor(String author) {
 565                 // FIXME TODO parsen und deduplizieren
 566                 Team team = Team.NewTitledInstance(author, author);
 567                 return team;
 568         }
 569
 570
 571         /**
 572          * Use same TaxonDescription if two records belong to the same taxon
 573          * @param state
 574          * @param newTaxonId
 575          * @param oldTaxonId
 576          * @param oldDescription
 577          * @param taxonMap
 578          * @return
 579          */
 580         protected TaxonDescription getTaxonDescription(AlgaTerraImportState state, Taxon taxon, Reference<?> sourceSec){
 581                 TaxonDescription result = null;
 582                 Set<TaxonDescription> descriptionSet= taxon.getDescriptions();
 583                 if (descriptionSet.size() > 0) {
 584                         result = descriptionSet.iterator().next();
 585                 }else{
 586                         result = TaxonDescription.NewInstance();
 587                         result.setTitleCache(sourceSec.getTitleCache(), true);
 588                         taxon.addDescription(result);
 589                 }
 590                 return result;
 591         }
 592
 593
 594
 595
 596 }