cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/DescriptiveDataSetService.java

   1 package eu.etaxonomy.cdm.api.service;
   2
   3 import java.io.Serializable;
   4 import java.util.ArrayList;
   5 import java.util.Arrays;
   6 import java.util.Collection;
   7 import java.util.HashMap;
   8 import java.util.HashSet;
   9 import java.util.List;
  10 import java.util.Map;
  11 import java.util.Set;
  12 import java.util.UUID;
  13
  14 import org.apache.log4j.Logger;
  15 import org.springframework.beans.factory.annotation.Autowired;
  16 import org.springframework.stereotype.Service;
  17 import org.springframework.transaction.annotation.Transactional;
  18
  19 import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
  20 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  21 import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
  22 import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;
  23 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  24 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  25 import eu.etaxonomy.cdm.model.common.Language;
  26 import eu.etaxonomy.cdm.model.description.CategoricalData;
  27 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  28 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  29 import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
  30 import eu.etaxonomy.cdm.model.description.DescriptiveSystemRole;
  31 import eu.etaxonomy.cdm.model.description.Feature;
  32 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  33 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  34 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  35 import eu.etaxonomy.cdm.model.description.TextData;
  36 import eu.etaxonomy.cdm.model.location.NamedArea;
  37 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  38 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  39 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  40 import eu.etaxonomy.cdm.model.taxon.Taxon;
  41 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  42 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  43 import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao;
  44 import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
  45 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  46 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  47
  48 @Service
  49 @Transactional(readOnly = false)
  50 public class DescriptiveDataSetService
  51         extends IdentifiableServiceBase<DescriptiveDataSet, IDescriptiveDataSetDao>
  52         implements IDescriptiveDataSetService {
  53
  54     private static Logger logger = Logger.getLogger(DescriptiveDataSetService.class);
  55
  56     @Autowired
  57     private IOccurrenceService occurrenceService;
  58
  59     @Autowired
  60     private IDescriptionService descriptionService;
  61
  62     @Autowired
  63     private ITaxonNodeService taxonNodeService;
  64
  65     @Autowired
  66     private IProgressMonitorService progressMonitorService;
  67
  68         @Override
  69         @Autowired
  70         protected void setDao(IDescriptiveDataSetDao dao) {
  71                 this.dao = dao;
  72         }
  73
  74         @Override
  75     public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,     Integer pageNumber,
  76                         List<String> propertyPaths) {
  77                 return dao.getDescriptionElements(descriptiveDataSet, features, pageSize, pageNumber, propertyPaths);
  78         }
  79
  80         @Override
  81         public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(
  82                         Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
  83                 return dao.getTaxonFeatureDescriptionElementMap(clazz, descriptiveDataSetUuid, role);
  84         }
  85
  86         @Override
  87     public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {
  88         return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern);
  89     }
  90
  91
  92     @Override
  93     @Transactional
  94     public UUID monitGetRowWrapper(DescriptiveDataSet descriptiveDataSet) {
  95         RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {
  96             @Override
  97             public Serializable doRun(IRemotingProgressMonitor monitor) {
  98                 return getRowWrapper(descriptiveDataSet, monitor);
  99             }
 100         };
 101         UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);
 102         monitorThread.setPriority(3);
 103         monitorThread.start();
 104         return uuid;
 105     }
 106
 107         @Override
 108         public ArrayList<RowWrapperDTO> getRowWrapper(DescriptiveDataSet descriptiveDataSet, IProgressMonitor monitor) {
 109             monitor.beginTask("Load row wrapper", descriptiveDataSet.getDescriptions().size());
 110             ArrayList<RowWrapperDTO> wrappers = new ArrayList<>();
 111             Set<DescriptionBase> descriptions = descriptiveDataSet.getDescriptions();
 112             for (DescriptionBase description : descriptions) {
 113             if(monitor.isCanceled()){
 114                 return new ArrayList<>();
 115             }
 116             wrappers.add(createRowWrapper(null, description, null, descriptiveDataSet));
 117             monitor.worked(1);
 118         }
 119             return wrappers;
 120         }
 121
 122     @Override
 123     public Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet){
 124         //set filter parameters
 125         TaxonNodeFilter filter = TaxonNodeFilter.NewRankInstance(descriptiveDataSet.getMinRank(), descriptiveDataSet.getMaxRank());
 126         descriptiveDataSet.getGeoFilter().forEach(area -> filter.orArea(area.getUuid()));
 127         descriptiveDataSet.getTaxonSubtreeFilter().forEach(node -> filter.orSubtree(node));
 128         filter.setIncludeUnpublished(true);
 129
 130         List<UUID> filteredNodes = taxonNodeService.uuidList(filter);
 131         return occurrenceService.listUuidAndTitleCacheByAssociatedTaxon(filteredNodes, null, null);
 132     }
 133
 134     @Override
 135     public RowWrapperDTO createRowWrapper(DescriptionBase description, DescriptiveDataSet descriptiveDataSet){
 136         return createRowWrapper(null, description, null, descriptiveDataSet);
 137     }
 138
 139     @Override
 140     public RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptiveDataSet descriptiveDataSet){
 141         return createRowWrapper(specimen, null, null, descriptiveDataSet);
 142     }
 143
 144         private RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptionBase description, TaxonNode taxonNode, DescriptiveDataSet descriptiveDataSet){
 145             if(description!=null){
 146                 specimen = description.getDescribedSpecimenOrObservation();
 147             }
 148         FieldUnit fieldUnit = null;
 149         String identifier = null;
 150         NamedArea country = null;
 151         //supplemental information
 152         if(specimen!=null){
 153             if(taxonNode==null){
 154                 Collection<TaxonBase<?>> associatedTaxa = occurrenceService.listAssociatedTaxa(specimen, null, null, null,
 155                         Arrays.asList(new String[]{
 156                                 "taxonNodes",
 157                                 "taxonNodes.classification",
 158                         }));
 159                 if(associatedTaxa!=null && !associatedTaxa.isEmpty()){
 160                     //FIXME: what about multiple associated taxa
 161                     Set<TaxonNode> taxonSubtreeFilter = descriptiveDataSet.getTaxonSubtreeFilter();
 162                     if(taxonSubtreeFilter!=null && !taxonSubtreeFilter.isEmpty()){
 163                         Taxon taxon = HibernateProxyHelper.deproxy(associatedTaxa.iterator().next(), Taxon.class);
 164                         taxonNode = taxon.getTaxonNode(taxonSubtreeFilter.iterator().next().getClassification());
 165                     }
 166                 }
 167             }
 168             Collection<FieldUnit> fieldUnits = occurrenceService.findFieldUnits(specimen.getUuid(),
 169                     Arrays.asList(new String[]{
 170                             "gatheringEvent",
 171                             "gatheringEvent.country"
 172                             }));
 173             if(fieldUnits.size()!=1){
 174                 logger.error("More than one or no field unit found for specimen"); //$NON-NLS-1$
 175             }
 176             else{
 177                 fieldUnit = fieldUnits.iterator().next();
 178             }
 179             if(specimen instanceof DerivedUnit){
 180                 identifier = occurrenceService.getMostSignificantIdentifier(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
 181             }
 182             if(fieldUnit!=null && fieldUnit.getGatheringEvent()!=null){
 183                 country = fieldUnit.getGatheringEvent().getCountry();
 184             }
 185         }
 186         return new RowWrapperDTO(description, specimen, taxonNode, fieldUnit, identifier, country);
 187         }
 188
 189     @Override
 190     @Transactional(readOnly = false)
 191     public void updateTitleCache(Class<? extends DescriptiveDataSet> clazz, Integer stepSize,
 192             IIdentifiableEntityCacheStrategy<DescriptiveDataSet> cacheStrategy, IProgressMonitor monitor) {
 193         if (clazz == null) {
 194             clazz = DescriptiveDataSet.class;
 195         }
 196         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 197     }
 198
 199     @Override
 200     public SpecimenDescription findDescriptionForDescriptiveDataSet(UUID descriptiveDataSetUuid, UUID specimenUuid){
 201         DescriptiveDataSet dataSet = load(descriptiveDataSetUuid);
 202         SpecimenOrObservationBase specimen = occurrenceService.load(specimenUuid);
 203
 204         Set<Feature> datasetFeatures = dataSet.getDescriptiveSystem().getDistinctFeatures();
 205         List<DescriptionElementBase> matchingDescriptionElements = new ArrayList<>();
 206
 207         for (SpecimenDescription specimenDescription : (Set<SpecimenDescription>) specimen.getDescriptions()) {
 208             specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescription.getUuid());
 209
 210             //check if description is already added to data set
 211             if(dataSet.getDescriptions().contains(specimenDescription)){
 212                 return specimenDescription;
 213             }
 214
 215             //gather specimen description features and check for match with dataset features
 216             Set<Feature> specimenDescriptionFeatures = new HashSet<>();
 217             for (DescriptionElementBase specimenDescriptionElement : specimenDescription.getElements()) {
 218                 Feature feature = specimenDescriptionElement.getFeature();
 219                 specimenDescriptionFeatures.add(feature);
 220                 if(datasetFeatures.contains(feature)){
 221                     matchingDescriptionElements.add(specimenDescriptionElement);
 222                 }
 223             }
 224         }
 225         //Create new specimen description if description has not already been added to the dataset
 226         SpecimenDescription newDesription = SpecimenDescription.NewInstance(specimen);
 227         newDesription.setTitleCache("Dataset "+dataSet.getLabel()+": "+newDesription.generateTitle(), true); //$NON-NLS-2$
 228
 229         //check for equals description element (same feature and same values)
 230         Map<Feature, List<DescriptionElementBase>> featureToElementMap = new HashMap<>();
 231         for(DescriptionElementBase element:matchingDescriptionElements){
 232             List<DescriptionElementBase> list = featureToElementMap.get(element.getFeature());
 233             if(list==null){
 234                 list = new ArrayList<>();
 235             }
 236             list.add(element);
 237             featureToElementMap.put(element.getFeature(), list);
 238         }
 239         Set<DescriptionElementBase> descriptionElementsToClone = new HashSet<>();
 240         for(Feature feature:featureToElementMap.keySet()){
 241             List<DescriptionElementBase> elements = featureToElementMap.get(feature);
 242             //no duplicate description elements found for this feature
 243             if(elements.size()==1){
 244                 descriptionElementsToClone.add(elements.get(0));
 245             }
 246             //duplicates found -> check if all are equal
 247             else{
 248                 DescriptionElementBase match = null;
 249                 for (DescriptionElementBase descriptionElementBase : elements) {
 250                     if(match==null){
 251                         match = descriptionElementBase;
 252                     }
 253                     else if(!new DescriptionElementCompareWrapper(match).equals(new DescriptionElementCompareWrapper(descriptionElementBase))){
 254                         match = null;
 255                         //TODO: propagate message
 256 //                        MessagingUtils.informationDialog(Messages.CharacterMatrix_MULTIPLE_DATA,
 257 //                                String.format(Messages.CharacterMatrix_MULTIPLE_DATA_MESSAGE, feature.getLabel()));
 258                         break;
 259                     }
 260                 }
 261                 if(match!=null){
 262                     descriptionElementsToClone.add(match);
 263                 }
 264             }
 265         }
 266         //clone matching descriptionElements
 267         for (DescriptionElementBase descriptionElementBase : descriptionElementsToClone) {
 268             DescriptionElementBase clone;
 269             try {
 270                 clone = descriptionElementBase.clone(newDesription);
 271                 clone.getSources().forEach(source -> {
 272                     if(descriptionElementBase instanceof CategoricalData){
 273                         TextData label = new DefaultCategoricalDescriptionBuilder().build((CategoricalData) descriptionElementBase, null);
 274                         source.setOriginalNameString(label.getText(Language.DEFAULT()));
 275                     }
 276                     else if(descriptionElementBase instanceof QuantitativeData){
 277                         TextData label = new DefaultQuantitativeDescriptionBuilder().build((QuantitativeData) descriptionElementBase, null);
 278                         source.setOriginalNameString(label.getText(Language.DEFAULT()));
 279                     }
 280                 });
 281             } catch (CloneNotSupportedException e) {
 282 //                MessagingUtils.error(CharacterMatrix.class, e);
 283             }
 284         }
 285
 286         //add all remaining description elements to the new description
 287         for(Feature wsFeature:datasetFeatures){
 288             boolean featureFound = false;
 289             for(DescriptionElementBase element:newDesription.getElements()){
 290                 if(element.getFeature().equals(wsFeature)){
 291                     featureFound = true;
 292                     break;
 293                 }
 294             }
 295             if(!featureFound){
 296                 if(wsFeature.isSupportsCategoricalData()){
 297                     newDesription.addElement(CategoricalData.NewInstance(wsFeature));
 298                 }
 299                 else if(wsFeature.isSupportsQuantitativeData()){
 300                     newDesription.addElement(QuantitativeData.NewInstance(wsFeature));
 301                 }
 302             }
 303         }
 304         return newDesription;
 305
 306     }
 307
 308     //TODO: this should either be solved in the model class itself
 309     //OR this should cover all possibilities including modifiers for example
 310     private class DescriptionElementCompareWrapper {
 311
 312         private DescriptionElementBase element;
 313         private Set<UUID> stateUuids = new HashSet<>();
 314         private Set<Float> avgs = new HashSet<>();
 315         private Set<Float> exacts = new HashSet<>();
 316         private Set<Float> maxs = new HashSet<>();
 317         private Set<Float> mins = new HashSet<>();
 318         private Set<Float> sampleSizes = new HashSet<>();
 319         private Set<Float> standardDevs = new HashSet<>();
 320         private Set<Float> lowerBounds = new HashSet<>();
 321         private Set<Float> upperBounds = new HashSet<>();
 322         private Set<Float> variances = new HashSet<>();
 323
 324         public DescriptionElementCompareWrapper(DescriptionElementBase element) {
 325             this.element = element;
 326             if(element.isInstanceOf(CategoricalData.class)){
 327                 CategoricalData elementData = (CategoricalData)element;
 328                 elementData.getStatesOnly().forEach(state->stateUuids.add(state.getUuid()));
 329             }
 330             else if(element.isInstanceOf(QuantitativeData.class)){
 331                 QuantitativeData elementData = (QuantitativeData)element;
 332                 elementData.getStatisticalValues().forEach(value->{
 333                     if(value.getType().equals(StatisticalMeasure.AVERAGE())){
 334                         avgs.add(value.getValue());
 335                     }
 336                     else if(value.getType().equals(StatisticalMeasure.EXACT_VALUE())){
 337                         exacts.add(value.getValue());
 338
 339                     }
 340                     else if(value.getType().equals(StatisticalMeasure.MAX())){
 341                         maxs.add(value.getValue());
 342                     }
 343                     else if(value.getType().equals(StatisticalMeasure.MIN())){
 344                         mins.add(value.getValue());
 345                     }
 346                     else if(value.getType().equals(StatisticalMeasure.SAMPLE_SIZE())){
 347                         sampleSizes.add(value.getValue());
 348
 349                     }
 350                     else if(value.getType().equals(StatisticalMeasure.STANDARD_DEVIATION())){
 351                         standardDevs.add(value.getValue());
 352                     }
 353                     else if(value.getType().equals(StatisticalMeasure.TYPICAL_LOWER_BOUNDARY())){
 354                         lowerBounds.add(value.getValue());
 355
 356                     }
 357                     else if(value.getType().equals(StatisticalMeasure.TYPICAL_UPPER_BOUNDARY())){
 358                         upperBounds.add(value.getValue());
 359                     }
 360                     else if(value.getType().equals(StatisticalMeasure.VARIANCE())){
 361                         variances.add(value.getValue());
 362                     }
 363                 });
 364             }
 365         }
 366
 367         @Override
 368         public int hashCode() {
 369             final int prime = 31;
 370             int result = 1;
 371             result = prime * result + getOuterType().hashCode();
 372             result = prime * result + ((avgs == null) ? 0 : avgs.hashCode());
 373             result = prime * result + ((element == null) ? 0 : element.hashCode());
 374             result = prime * result + ((exacts == null) ? 0 : exacts.hashCode());
 375             result = prime * result + ((lowerBounds == null) ? 0 : lowerBounds.hashCode());
 376             result = prime * result + ((maxs == null) ? 0 : maxs.hashCode());
 377             result = prime * result + ((mins == null) ? 0 : mins.hashCode());
 378             result = prime * result + ((sampleSizes == null) ? 0 : sampleSizes.hashCode());
 379             result = prime * result + ((standardDevs == null) ? 0 : standardDevs.hashCode());
 380             result = prime * result + ((stateUuids == null) ? 0 : stateUuids.hashCode());
 381             result = prime * result + ((upperBounds == null) ? 0 : upperBounds.hashCode());
 382             result = prime * result + ((variances == null) ? 0 : variances.hashCode());
 383             return result;
 384         }
 385
 386         @Override
 387         public boolean equals(Object obj) {
 388             if (this == obj) {
 389                 return true;
 390             }
 391             if (obj == null) {
 392                 return false;
 393             }
 394             if (getClass() != obj.getClass()) {
 395                 return false;
 396             }
 397             DescriptionElementCompareWrapper other = (DescriptionElementCompareWrapper) obj;
 398             if (!getOuterType().equals(other.getOuterType())) {
 399                 return false;
 400             }
 401             if (avgs == null) {
 402                 if (other.avgs != null) {
 403                     return false;
 404                 }
 405             } else if (!avgs.equals(other.avgs)) {
 406                 return false;
 407             }
 408             if (element == null) {
 409                 if (other.element != null) {
 410                     return false;
 411                 }
 412             } else if (!element.equals(other.element)) {
 413                 return false;
 414             }
 415             if (exacts == null) {
 416                 if (other.exacts != null) {
 417                     return false;
 418                 }
 419             } else if (!exacts.equals(other.exacts)) {
 420                 return false;
 421             }
 422             if (lowerBounds == null) {
 423                 if (other.lowerBounds != null) {
 424                     return false;
 425                 }
 426             } else if (!lowerBounds.equals(other.lowerBounds)) {
 427                 return false;
 428             }
 429             if (maxs == null) {
 430                 if (other.maxs != null) {
 431                     return false;
 432                 }
 433             } else if (!maxs.equals(other.maxs)) {
 434                 return false;
 435             }
 436             if (mins == null) {
 437                 if (other.mins != null) {
 438                     return false;
 439                 }
 440             } else if (!mins.equals(other.mins)) {
 441                 return false;
 442             }
 443             if (sampleSizes == null) {
 444                 if (other.sampleSizes != null) {
 445                     return false;
 446                 }
 447             } else if (!sampleSizes.equals(other.sampleSizes)) {
 448                 return false;
 449             }
 450             if (standardDevs == null) {
 451                 if (other.standardDevs != null) {
 452                     return false;
 453                 }
 454             } else if (!standardDevs.equals(other.standardDevs)) {
 455                 return false;
 456             }
 457             if (stateUuids == null) {
 458                 if (other.stateUuids != null) {
 459                     return false;
 460                 }
 461             } else if (!stateUuids.equals(other.stateUuids)) {
 462                 return false;
 463             }
 464             if (upperBounds == null) {
 465                 if (other.upperBounds != null) {
 466                     return false;
 467                 }
 468             } else if (!upperBounds.equals(other.upperBounds)) {
 469                 return false;
 470             }
 471             if (variances == null) {
 472                 if (other.variances != null) {
 473                     return false;
 474                 }
 475             } else if (!variances.equals(other.variances)) {
 476                 return false;
 477             }
 478             return true;
 479         }
 480
 481         private DescriptiveDataSetService getOuterType() {
 482             return DescriptiveDataSetService.this;
 483         }
 484
 485     }
 486
 487 }