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.List;
   8 import java.util.Map;
   9 import java.util.Set;
  10 import java.util.UUID;
  11
  12 import org.apache.log4j.Logger;
  13 import org.springframework.beans.factory.annotation.Autowired;
  14 import org.springframework.stereotype.Service;
  15 import org.springframework.transaction.annotation.Transactional;
  16
  17 import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO;
  18 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  19 import eu.etaxonomy.cdm.common.monitor.IRemotingProgressMonitor;
  20 import eu.etaxonomy.cdm.common.monitor.RemotingProgressMonitorThread;
  21 import eu.etaxonomy.cdm.filter.TaxonNodeFilter;
  22 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  23 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  24 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  25 import eu.etaxonomy.cdm.model.description.DescriptiveDataSet;
  26 import eu.etaxonomy.cdm.model.description.DescriptiveSystemRole;
  27 import eu.etaxonomy.cdm.model.description.Feature;
  28 import eu.etaxonomy.cdm.model.location.NamedArea;
  29 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  30 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  31 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  32 import eu.etaxonomy.cdm.model.taxon.Taxon;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  35 import eu.etaxonomy.cdm.persistence.dao.description.IDescriptiveDataSetDao;
  36 import eu.etaxonomy.cdm.persistence.dto.SpecimenNodeWrapper;
  37 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  38 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  39
  40 @Service
  41 @Transactional(readOnly = false)
  42 public class DescriptiveDataSetService
  43         extends IdentifiableServiceBase<DescriptiveDataSet, IDescriptiveDataSetDao>
  44         implements IDescriptiveDataSetService {
  45
  46     private static Logger logger = Logger.getLogger(DescriptiveDataSetService.class);
  47
  48     @Autowired
  49     private IOccurrenceService occurrenceService;
  50
  51     @Autowired
  52     private ITaxonNodeService taxonNodeService;
  53
  54     @Autowired
  55     private IProgressMonitorService progressMonitorService;
  56
  57         @Override
  58         @Autowired
  59         protected void setDao(IDescriptiveDataSetDao dao) {
  60                 this.dao = dao;
  61         }
  62
  63         @Override
  64     public Map<DescriptionBase, Set<DescriptionElementBase>> getDescriptionElements(DescriptiveDataSet descriptiveDataSet, Set<Feature> features, Integer pageSize,     Integer pageNumber,
  65                         List<String> propertyPaths) {
  66                 return dao.getDescriptionElements(descriptiveDataSet, features, pageSize, pageNumber, propertyPaths);
  67         }
  68
  69         @Override
  70         public <T extends DescriptionElementBase> Map<UuidAndTitleCache, Map<UUID, Set<T>>> getTaxonFeatureDescriptionElementMap(
  71                         Class<T> clazz, UUID descriptiveDataSetUuid, DescriptiveSystemRole role) {
  72                 return dao.getTaxonFeatureDescriptionElementMap(clazz, descriptiveDataSetUuid, role);
  73         }
  74
  75         @Override
  76     public List<UuidAndTitleCache<DescriptiveDataSet>> getDescriptiveDataSetUuidAndTitleCache(Integer limitOfInitialElements, String pattern) {
  77         return dao.getDescriptiveDataSetUuidAndTitleCache( limitOfInitialElements, pattern);
  78     }
  79
  80
  81     @Override
  82     @Transactional
  83     public UUID monitGetRowWrapper(DescriptiveDataSet descriptiveDataSet) {
  84         RemotingProgressMonitorThread monitorThread = new RemotingProgressMonitorThread() {
  85             @Override
  86             public Serializable doRun(IRemotingProgressMonitor monitor) {
  87                 return getRowWrapper(descriptiveDataSet, monitor);
  88             }
  89         };
  90         UUID uuid = progressMonitorService.registerNewRemotingMonitor(monitorThread);
  91         monitorThread.setPriority(3);
  92         monitorThread.start();
  93         return uuid;
  94     }
  95
  96         @Override
  97         public ArrayList<RowWrapperDTO> getRowWrapper(DescriptiveDataSet descriptiveDataSet, IProgressMonitor monitor) {
  98             monitor.beginTask("Load row wrapper", descriptiveDataSet.getDescriptions().size());
  99             ArrayList<RowWrapperDTO> wrappers = new ArrayList<>();
 100             Set<DescriptionBase> descriptions = descriptiveDataSet.getDescriptions();
 101             for (DescriptionBase description : descriptions) {
 102             if(monitor.isCanceled()){
 103                 return new ArrayList<>();
 104             }
 105             wrappers.add(createRowWrapper(null, description, null, descriptiveDataSet));
 106             monitor.worked(1);
 107         }
 108             return wrappers;
 109         }
 110
 111     @Override
 112     public Collection<SpecimenNodeWrapper> loadSpecimens(DescriptiveDataSet descriptiveDataSet){
 113         //set filter parameters
 114         TaxonNodeFilter filter = TaxonNodeFilter.NewRankInstance(descriptiveDataSet.getMinRank(), descriptiveDataSet.getMaxRank());
 115         descriptiveDataSet.getGeoFilter().forEach(area -> filter.orArea(area.getUuid()));
 116         descriptiveDataSet.getTaxonSubtreeFilter().forEach(node -> filter.orSubtree(node));
 117         filter.setIncludeUnpublished(true);
 118
 119         List<UUID> filteredNodes = taxonNodeService.uuidList(filter);
 120         return occurrenceService.listUuidAndTitleCacheByAssociatedTaxon(filteredNodes, null, null);
 121     }
 122
 123     @Override
 124     public RowWrapperDTO createRowWrapper(DescriptionBase description, DescriptiveDataSet descriptiveDataSet){
 125         return createRowWrapper(null, description, null, descriptiveDataSet);
 126     }
 127
 128     @Override
 129     public RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptiveDataSet descriptiveDataSet){
 130         return createRowWrapper(specimen, null, null, descriptiveDataSet);
 131     }
 132
 133         private RowWrapperDTO createRowWrapper(SpecimenOrObservationBase specimen, DescriptionBase description, TaxonNode taxonNode, DescriptiveDataSet descriptiveDataSet){
 134             if(description!=null){
 135                 specimen = description.getDescribedSpecimenOrObservation();
 136             }
 137         FieldUnit fieldUnit = null;
 138         String identifier = null;
 139         NamedArea country = null;
 140         //supplemental information
 141         if(specimen!=null){
 142             if(taxonNode==null){
 143                 Collection<TaxonBase<?>> associatedTaxa = occurrenceService.listAssociatedTaxa(specimen, null, null, null,
 144                         Arrays.asList(new String[]{
 145                                 "taxonNodes",
 146                                 "taxonNodes.classification",
 147                         }));
 148                 if(associatedTaxa!=null){
 149                     //FIXME: what about multiple associated taxa
 150                     Set<TaxonNode> taxonSubtreeFilter = descriptiveDataSet.getTaxonSubtreeFilter();
 151                     if(taxonSubtreeFilter!=null && !taxonSubtreeFilter.isEmpty()){
 152                         Taxon taxon = HibernateProxyHelper.deproxy(associatedTaxa.iterator().next(), Taxon.class);
 153                         taxonNode = taxon.getTaxonNode(taxonSubtreeFilter.iterator().next().getClassification());
 154                     }
 155                 }
 156             }
 157             Collection<FieldUnit> fieldUnits = occurrenceService.getFieldUnits(specimen.getUuid(),
 158                     Arrays.asList(new String[]{
 159                             "gatheringEvent",
 160                             "gatheringEvent.country"
 161                             }));
 162             if(fieldUnits.size()!=1){
 163                 logger.error("More than one or no field unit found for specimen"); //$NON-NLS-1$
 164             }
 165             else{
 166                 fieldUnit = fieldUnits.iterator().next();
 167             }
 168             if(specimen instanceof DerivedUnit){
 169                 identifier = occurrenceService.getMostSignificantIdentifier(HibernateProxyHelper.deproxy(specimen, DerivedUnit.class));
 170             }
 171             if(fieldUnit!=null && fieldUnit.getGatheringEvent()!=null){
 172                 country = fieldUnit.getGatheringEvent().getCountry();
 173             }
 174         }
 175         return new RowWrapperDTO(description, specimen, taxonNode, fieldUnit, identifier, country);
 176         }
 177
 178     @Override
 179     @Transactional(readOnly = false)
 180     public void updateTitleCache(Class<? extends DescriptiveDataSet> clazz, Integer stepSize,
 181             IIdentifiableEntityCacheStrategy<DescriptiveDataSet> cacheStrategy, IProgressMonitor monitor) {
 182         if (clazz == null) {
 183             clazz = DescriptiveDataSet.class;
 184         }
 185         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 186     }
 187
 188 }