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.Set;
  17 import java.util.UUID;
  18
  19 import org.apache.commons.lang.StringUtils;
  20 import org.apache.log4j.Logger;
  21 import org.springframework.transaction.TransactionStatus;
  22
  23 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  24 import eu.etaxonomy.cdm.io.berlinModel.in.BerlinModelImportBase;
  25 import eu.etaxonomy.cdm.io.common.ResultSetPartitioner;
  26 import eu.etaxonomy.cdm.io.common.Source;
  27 import eu.etaxonomy.cdm.model.agent.Team;
  28 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  29 import eu.etaxonomy.cdm.model.common.TimePeriod;
  30 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  31 import eu.etaxonomy.cdm.model.description.Feature;
  32 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  33 import eu.etaxonomy.cdm.model.description.State;
  34 import eu.etaxonomy.cdm.model.location.NamedArea;
  35 import eu.etaxonomy.cdm.model.location.Point;
  36 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  37 import eu.etaxonomy.cdm.model.location.TdwgArea;
  38 import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
  39 import eu.etaxonomy.cdm.model.occurrence.Collection;
  40
  41 /**
  42  * @author a.mueller
  43  * @created 12.09.2012
  44  */
  45 public abstract class AlgaTerraSpecimenImportBase extends BerlinModelImportBase{
  46         private static final Logger logger = Logger.getLogger(AlgaTerraSpecimenImportBase.class);
  47
  48         public static final String ECO_FACT_FIELD_OBSERVATION_NAMESPACE = "EcoFact";
  49         public static final String ECO_FACT_DERIVED_UNIT_NAMESPACE = "EcoFact";
  50         public static final String TYPE_SPECIMEN_FIELD_OBSERVATION_NAMESPACE = "TypeSpecimen_FieldObservation";
  51         public static final String TYPE_SPECIMEN_DERIVED_UNIT_NAMESPACE = "TypeSpecimen_DerivedUnit";
  52
  53         public static final String TERMS_NAMESPACE = "ALGA_TERRA_TERMS";
  54
  55         //TODO move to transformrer
  56         final static UUID uuidMarkerAlkalinity = UUID.fromString("e52d0ea2-0c1f-4d95-ae6d-e21ab317c594");
  57         final static UUID uuidRefSystemGps = UUID.fromString("c23e4928-c137-4e4a-b6ab-b430da3d0b94");
  58         final static UUID uuidFeatureSpecimenCommunity = UUID.fromString("3ff5b1ab-3999-4b5a-b8f7-01fd2f6c12c7");
  59         final static UUID uuidFeatureAdditionalData = UUID.fromString("0ac82ab8-2c2b-4953-98eb-a9f718eb9c57");
  60         final static UUID uuidFeatureHabitatExplanation = UUID.fromString("6fe32295-61a3-44fc-9fcf-a85790ea888f");
  61
  62         final static UUID uuidVocAlgaTerraClimate = UUID.fromString("b0a677c6-8bb6-43f4-b1b8-fc377a10feb5");
  63         final static UUID uuidVocAlgaTerraHabitat = UUID.fromString("06f30114-e19c-4e7d-a8e5-5488c41fcbc5");
  64         final static UUID uuidVocAlgaTerraLifeForm = UUID.fromString("3c0b194e-809c-4b42-9498-6ff034066ed7");
  65
  66         final static UUID uuidFeatureAlgaTerraClimate = UUID.fromString("8754674c-9ab9-4f28-95f1-91eeee2314ee");
  67         final static UUID uuidFeatureAlgaTerraHabitat = UUID.fromString("7def3fc2-cdc5-4739-8e13-62edbd053415");
  68         final static UUID uuidFeatureAlgaTerraLifeForm = UUID.fromString("9b657901-1b0d-4a2a-8d21-dd8c1413e2e6");
  69
  70         final static UUID uuidVocParameter = UUID.fromString("45888b40-5bbb-4293-aa1e-02479796cd7c");
  71         final static UUID uuidStatMeasureSingleValue = UUID.fromString("eb4c3d98-4d4b-4c37-8eb4-17315ce79920");
  72         final static UUID uuidMeasurementValueModifier = UUID.fromString("0218a7a3-f6c0-4d06-a4f8-6b50b73aef5e");
  73
  74         final static UUID uuidModifierLowerThan = UUID.fromString("2b500085-6bef-4003-b6ea-e0ad0237d79d");
  75         final static UUID uuidModifierGreaterThan = UUID.fromString("828df49d-c745-48f7-b083-0ada43356c34");
  76
  77
  78         /**
  79          * Creates the vocabularies and the features for Climate, Habitat and Lifeform
  80          * @param state
  81          * @throws SQLException
  82          */
  83         protected void makeVocabulariesAndFeatures(AlgaTerraImportState state) throws SQLException {
  84                 String abbrevLabel = null;
  85                 URI uri = null;
  86
  87                 if (! state.isSpecimenVocabulariesCreated()){
  88
  89                         TransactionStatus txStatus = this.startTransaction();
  90
  91                         boolean isOrdered = true;
  92                         OrderedTermVocabulary<State> climateVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraClimate, "Climate", "Climate", abbrevLabel, uri, isOrdered, null);
  93                         OrderedTermVocabulary<State> habitatVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraHabitat, "Habitat", "Habitat", abbrevLabel, uri, isOrdered, null);
  94                         OrderedTermVocabulary<State> lifeformVoc = (OrderedTermVocabulary)getVocabulary(uuidVocAlgaTerraLifeForm, "Lifeform", "Lifeform", abbrevLabel, uri, isOrdered, null);
  95
  96
  97                         Feature feature = getFeature(state, uuidFeatureAlgaTerraClimate, "Climate","Climate", null, null);
  98                         feature.setSupportsCategoricalData(true);
  99
 100                         feature = getFeature(state, uuidFeatureAlgaTerraLifeForm, "LifeForm","LifeForm", null, null);
 101                         feature.setSupportsCategoricalData(true);
 102
 103                         feature = Feature.HABITAT();
 104                         feature.setSupportsCategoricalData(true);
 105                         getTermService().saveOrUpdate(feature);
 106
 107                         Source source = state.getAlgaTerraConfigurator().getSource();
 108
 109                         String climateSql = "SELECT * FROM EcoClimate";
 110                         ResultSet rs = source.getResultSet(climateSql);
 111                         while (rs.next()){
 112                                 String climate = rs.getString("Climate");
 113                                 String description = rs.getString("Description");
 114                                 Integer id = rs.getInt("ClimateId");
 115                                 UUID uuid = UUID.fromString(rs.getString("UUID"));
 116                                 State stateTerm = getStateTerm(state, uuid, climate, description, null, climateVoc);
 117                                 addOriginalSource(stateTerm, id.toString(), "EcoClimate", state.getTransactionalSourceReference());
 118                                 getTermService().saveOrUpdate(stateTerm);
 119                         }
 120
 121                         String habitatSql = "SELECT * FROM EcoHabitat";
 122                         rs = source.getResultSet(habitatSql);
 123                         while (rs.next()){
 124                                 String habitat = rs.getString("Habitat");
 125                                 String description = rs.getString("Description");
 126                                 Integer id = rs.getInt("HabitatId");
 127                                 UUID uuid = UUID.fromString(rs.getString("UUID"));
 128                                 State stateTerm = getStateTerm(state, uuid, habitat, description, null, habitatVoc);
 129                                 addOriginalSource(stateTerm, id.toString(), "EcoHabitat", state.getTransactionalSourceReference());
 130                                 getTermService().saveOrUpdate(stateTerm);
 131                         }
 132
 133                         String lifeformSql = "SELECT * FROM EcoLifeForm";
 134                         rs = source.getResultSet(lifeformSql);
 135                         while (rs.next()){
 136                                 String lifeform = rs.getString("LifeForm");
 137                                 String description = rs.getString("Description");
 138                                 Integer id = rs.getInt("LifeFormId");
 139                                 UUID uuid = UUID.fromString(rs.getString("UUID"));
 140                                 State stateTerm = getStateTerm(state, uuid, lifeform, description, null, lifeformVoc);
 141                                 addOriginalSource(stateTerm, id.toString(), "EcoLifeForm", state.getTransactionalSourceReference());
 142                                 getTermService().saveOrUpdate(stateTerm);
 143                         }
 144
 145                         this.commitTransaction(txStatus);
 146
 147                         state.setSpecimenVocabulariesCreated(true);
 148                 }
 149
 150         }
 151
 152         protected String getLocalityString(){
 153                 return "Locality";
 154         }
 155
 156         protected void handleSingleSpecimen(ResultSet rs, DerivedUnitFacade facade, AlgaTerraImportState state, ResultSetPartitioner partitioner) throws SQLException {
 157                 //FIXME missing fields #3084, #3085, #3080
 158                 try {
 159
 160                         Integer unitId = nullSafeInt(rs, "unitId");
 161                         String locality = rs.getString(getLocalityString());
 162                         Double latitude = nullSafeDouble(rs, "Latitude");
 163                         Double longitude = nullSafeDouble(rs, "Longitude");
 164                         Integer errorRadius = nullSafeInt(rs,"Prec");
 165                         String geoCodeMethod = rs.getString("GeoCodeMethod");
 166
 167                         Integer altitude = nullSafeInt(rs, "Altitude");
 168                         Integer lowerAltitude = nullSafeInt(rs,"AltitudeLowerValue");
 169                         String altitudeUnit = rs.getString("AltitudeUnit");
 170                         Double depth = nullSafeDouble(rs, "Depth");
 171                         Double depthLow = nullSafeDouble(rs, "DepthLow");
 172
 173                         String collectorsNumber = rs.getString("CollectorsNumber");
 174                         Date collectionDateStart = rs.getDate("CollectionDate");
 175                         Date collectionDateEnd = rs.getDate("CollectionDateEnd");
 176
 177                         Integer collectionFk = nullSafeInt(rs,"CollectionFk");
 178
 179
 180                         //location
 181                         facade.setLocality(locality);
 182
 183                         //exact location
 184                         ReferenceSystem referenceSystem = makeRefrenceSystem(geoCodeMethod, state);
 185                         if (longitude != null || latitude != null || referenceSystem != null || errorRadius != null){
 186                                 Point exactLocation = Point.NewInstance(longitude, latitude, referenceSystem, errorRadius);
 187                                 facade.setExactLocation(exactLocation);
 188                         }
 189
 190                         //altitude, depth
 191                         if (StringUtils.isNotBlank(altitudeUnit) && ! altitudeUnit.trim().equalsIgnoreCase("m")){
 192                                 logger.warn("Altitude unit is not [m] but: " +  altitudeUnit);
 193                         }
 194                         if ( altitude != null){
 195                                 if (lowerAltitude == null){
 196                                         facade.setAbsoluteElevation(altitude);
 197                                 }else{
 198                                         if (! facade.isEvenDistance(lowerAltitude, altitude)){
 199                                                 //FIXME there is a ticket for this
 200                                                 altitude = altitude + 1;
 201                                                 logger.info("Current implementation of altitude does not allow uneven distances");
 202                                         }
 203                                         facade.setAbsoluteElevationRange(lowerAltitude,altitude);
 204                                 }
 205                         }
 206                         if ( depth != null){
 207                                 //FIXME needs model change to accept double #3072
 208                                 Integer intDepth = depth.intValue();
 209                                 if (depthLow == null){
 210                                         facade.setDistanceToWaterSurface(intDepth);
 211                                 }else{
 212                                         //FIXME range not yet in model #3074
 213                                         facade.setDistanceToWaterSurface(intDepth);
 214                                 }
 215                         }
 216
 217                         //field
 218                         facade.setFieldNumber(collectorsNumber);
 219                         TimePeriod gatheringPeriod = TimePeriod.NewInstance(collectionDateStart, collectionDateEnd);
 220                         facade.setGatheringPeriod(gatheringPeriod);
 221                         handleCollectorTeam(state, facade, rs);
 222
 223                         //areas
 224                         makeAreas(state, rs, facade);
 225
 226                         //collection
 227                         if (collectionFk != null){
 228                                 Collection subCollection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_SUBCOLLECTION, String.valueOf(collectionFk), Collection.class);
 229                                 if (subCollection != null){
 230                                         facade.setCollection(subCollection);
 231                                 }else{
 232                                         Collection collection = state.getRelatedObject(AlgaTerraCollectionImport.NAMESPACE_COLLECTION, String.valueOf(collectionFk), Collection.class);
 233                                         facade.setCollection(collection);
 234                                 }
 235                         }
 236
 237                         //notes
 238                         //TODO is this an annotation on field observation or on the derived unit?
 239
 240                         //TODO id, created for fact +  ecoFact
 241                         //      this.doIdCreatedUpdatedNotes(state, descriptionElement, rs, id, namespace);
 242                         if (unitId != null){
 243                                 this.doIdCreatedUpdatedNotes(state, facade.innerDerivedUnit(), rs, unitId, getDerivedUnitNameSpace());
 244                         }else{
 245                                 logger.warn("Specimen has no unitId: " +  facade.innerDerivedUnit() + ": " + getDerivedUnitNameSpace());
 246                         }
 247
 248
 249                 } catch (Exception e) {
 250                         throw new RuntimeException(e);
 251                 }
 252
 253         }
 254
 255         protected abstract String getDerivedUnitNameSpace();
 256
 257         protected DescriptionBase getFieldObservationDescription(DerivedUnitFacade facade) {
 258                 Set<DescriptionBase> descriptions = facade.innerFieldObservation().getDescriptions();
 259                 for (DescriptionBase desc : descriptions){
 260                         if (desc.isImageGallery() == false){
 261                                 return desc;
 262                         }
 263                 }
 264                 SpecimenDescription specDesc = SpecimenDescription.NewInstance(facade.innerFieldObservation());
 265                 descriptions.add(specDesc);
 266                 return specDesc;
 267         }
 268
 269
 270         private void makeAreas(AlgaTerraImportState state, ResultSet rs, DerivedUnitFacade facade) throws SQLException {
 271                 Object gazetteerId = rs.getObject("GazetteerId");
 272                 if (gazetteerId != null){
 273                         //TDWG
 274                         NamedArea tdwgArea;
 275                         String tdwg4 = rs.getString("L4Code");
 276                         if (isNotBlank(tdwg4)){
 277                                 tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg4);
 278                         }else{
 279                                 String tdwg3 = rs.getString("L3Code");
 280                                 if (isNotBlank(tdwg3)){
 281                                         tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(tdwg3);
 282                                 }else{
 283                                         Integer tdwg2 = rs.getInt("L2Code");
 284                                         tdwgArea = TdwgArea.getAreaByTdwgAbbreviation(String.valueOf(tdwg2));
 285                                 }
 286                         }
 287                         if (tdwgArea == null){
 288                                 logger.warn("TDWG area could not be defined for gazetterId: " + gazetteerId);
 289                         }else{
 290                                 facade.addCollectingArea(tdwgArea);
 291                         }
 292
 293                         //Countries
 294                         WaterbodyOrCountry country = null;
 295                         String isoCountry = rs.getString("ISOCountry");
 296                         String countryStr = rs.getString("Country");
 297                         if (isNotBlank(isoCountry)){
 298                                 country = WaterbodyOrCountry.getWaterbodyOrCountryByIso3166A2(isoCountry);
 299                         }else if (isNotBlank(countryStr)){
 300                                 logger.warn("Country exists but no ISO code");
 301                         }
 302                         if (country == null){
 303                                 logger.warn("Country does not exist for GazetteerID " + gazetteerId);
 304                         }else{
 305                                 facade.setCountry(country);
 306                         }
 307
 308                 }
 309
 310                 //Waterbody
 311                 WaterbodyOrCountry waterbody = null;
 312                 String waterbodyStr = rs.getString("WaterBody");
 313                 if (isNotBlank(waterbodyStr)){
 314                         if (waterbodyStr.equals("Atlantic Ocean")){
 315                                 waterbody = WaterbodyOrCountry.ATLANTICOCEAN();
 316                         }else{
 317                                 logger.warn("Waterbody not recognized: " + waterbody);
 318                         }
 319                         if (waterbody != null){
 320                                 facade.addCollectingArea(waterbody);
 321                         }
 322                 }
 323
 324
 325                 //countries sub
 326                 //TODO -> SpecimenImport (not existing in TypeSpecimen)
 327         }
 328
 329
 330
 331
 332         private ReferenceSystem makeRefrenceSystem(String geoCodeMethod, AlgaTerraImportState state) {
 333                 if (StringUtils.isBlank(geoCodeMethod)){
 334                         return null;
 335                 }else if(geoCodeMethod.startsWith("GPS")){
 336                         getReferenceSystem(state, uuidRefSystemGps, "GPS", "GPS", "GPS", ReferenceSystem.GOOGLE_EARTH().getVocabulary());
 337                         return ReferenceSystem.WGS84();
 338                 }else if(geoCodeMethod.startsWith("Google")){
 339                         return ReferenceSystem.GOOGLE_EARTH();
 340                 }else if(geoCodeMethod.startsWith("Map")){
 341                         logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");
 342                         return null;
 343                 }else if(geoCodeMethod.startsWith("WikiProjekt Georeferenzierung") || geoCodeMethod.startsWith("http://toolserver.org/~geohack/geohack.php") ){
 344                         return ReferenceSystem.WGS84();
 345                 }else {
 346                         logger.warn("Reference system " +  geoCodeMethod +  " not yet supported.");
 347                         return null;
 348                 }
 349         }
 350
 351
 352
 353
 354         private void handleCollectorTeam(AlgaTerraImportState state, DerivedUnitFacade facade, ResultSet rs) throws SQLException {
 355                 // FIXME parsen
 356                 String collector = rs.getString("Collector");
 357                 Team team = Team.NewTitledInstance(collector, collector);
 358                 facade.setCollector(team);
 359         }
 360
 361
 362
 363
 364 }