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

   1 // $Id$
   2 /**
   3  * Copyright (C) 2007 EDIT
   4  * European Distributed Institute of Taxonomy
   5  * http://www.e-taxonomy.eu
   6  *
   7  * The contents of this file are subject to the Mozilla Public License Version 1.1
   8  * See LICENSE.TXT at the top of this package for the full license terms.
   9  */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.util.ArrayList;
  14 import java.util.Arrays;
  15 import java.util.HashSet;
  16 import java.util.List;
  17 import java.util.Set;
  18
  19 import org.apache.log4j.Logger;
  20 import org.hibernate.Hibernate;
  21 import org.springframework.beans.factory.annotation.Autowired;
  22 import org.springframework.stereotype.Service;
  23 import org.springframework.transaction.annotation.Propagation;
  24 import org.springframework.transaction.annotation.Transactional;
  25
  26 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  27 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  28 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  29 import eu.etaxonomy.cdm.api.service.pager.Pager;
  30 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  31 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  32 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  33 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  34 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  35 import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
  36 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  37 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  38 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  39 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  40 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  41 import eu.etaxonomy.cdm.model.location.WaterbodyOrCountry;
  42 import eu.etaxonomy.cdm.model.media.Media;
  43 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  44 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  45 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  46 import eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase;
  47 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  48 import eu.etaxonomy.cdm.model.occurrence.FieldObservation;
  49 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  50 import eu.etaxonomy.cdm.model.taxon.Taxon;
  51 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  53 import eu.etaxonomy.cdm.persistence.dao.AbstractBeanInitializer;
  54 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  55 import eu.etaxonomy.cdm.persistence.dao.description.IDescriptionDao;
  56 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
  57 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  58 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  59 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  60
  61 /**
  62  * @author a.babadshanjan
  63  * @created 01.09.2008
  64  */
  65 @Service
  66 @Transactional(propagation = Propagation.SUPPORTS, readOnly = true)
  67 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
  68
  69     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
  70
  71     @Autowired
  72     private IDefinedTermDao definedTermDao;
  73
  74     @Autowired
  75     private IDescriptionService descriptionService;
  76
  77     @Autowired
  78     private ITaxonService taxonService;
  79
  80     @Autowired
  81     private AbstractBeanInitializer beanInitializer;
  82
  83     @Autowired
  84     private ITaxonDao taxonDao;
  85
  86
  87
  88     public OccurrenceServiceImpl() {
  89         logger.debug("Load OccurrenceService Bean");
  90     }
  91
  92
  93     /* (non-Javadoc)
  94      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
  95      */
  96     @Override
  97     @Transactional(readOnly = false)
  98     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
  99         if (clazz == null){
 100             clazz = SpecimenOrObservationBase.class;
 101         }
 102         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 103     }
 104
 105
 106     /**
 107      * FIXME Candidate for harmonization
 108      * move to termService
 109      */
 110     public WaterbodyOrCountry getCountryByIso(String iso639) {
 111         return this.definedTermDao.getCountryByIso(iso639);
 112
 113     }
 114
 115     /**
 116      * FIXME Candidate for harmonization
 117      * move to termService
 118      */
 119     public List<WaterbodyOrCountry> getWaterbodyOrCountryByName(String name) {
 120         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(WaterbodyOrCountry.class, name, null, null, null, null, null, null) ;
 121         List<WaterbodyOrCountry> countries = new ArrayList<WaterbodyOrCountry>();
 122         for (int i=0;i<terms.size();i++){
 123             countries.add((WaterbodyOrCountry)terms.get(i));
 124         }
 125         return countries;
 126     }
 127
 128     @Autowired
 129     protected void setDao(IOccurrenceDao dao) {
 130         this.dao = dao;
 131     }
 132
 133     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 134         Integer numberOfResults = dao.countDerivationEvents(occurence);
 135
 136         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 137         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 138             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 139         }
 140
 141         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 142     }
 143
 144     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 145         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 146
 147         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 148         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 149             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 150         }
 151
 152         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 153     }
 154
 155     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 156         Integer numberOfResults = dao.countMedia(occurence);
 157
 158         List<Media> results = new ArrayList<Media>();
 159         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 160             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 161         }
 162
 163         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 164     }
 165
 166     /* (non-Javadoc)
 167      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#list(java.lang.Class, eu.etaxonomy.cdm.model.taxon.TaxonBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 168      */
 169     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 170         Integer numberOfResults = dao.count(type,determinedAs);
 171         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 172         pageNumber = pageNumber == null ? 0 : pageNumber;
 173         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 174             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 175             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 176         }
 177         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 178     }
 179
 180     @Override
 181     public List<UuidAndTitleCache<DerivedUnitBase>> getDerivedUnitBaseUuidAndTitleCache() {
 182         return dao.getDerivedUnitBaseUuidAndTitleCache();
 183     }
 184
 185     @Override
 186     public List<UuidAndTitleCache<FieldObservation>> getFieldObservationUuidAndTitleCache() {
 187         return dao.getFieldObservationUuidAndTitleCache();
 188     }
 189
 190     /* (non-Javadoc)
 191      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnitBase)
 192      */
 193     @Override
 194     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnitBase derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 195         derivedUnit = (DerivedUnitBase<?>)dao.load(derivedUnit.getUuid(), null);
 196         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 197         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 198         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 199         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 200         return derivedUnitFacade;
 201     }
 202
 203     /* (non-Javadoc)
 204      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 205      */
 206     @Override
 207     public List<DerivedUnitFacade> listDerivedUnitFacades(
 208             DescriptionBase description, List<String> propertyPaths) {
 209
 210         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 211         IndividualsAssociation tempIndividualsAssociation;
 212         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 213         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 214         for(DescriptionElementBase element : elements){
 215             if(element instanceof IndividualsAssociation){
 216                 tempIndividualsAssociation = (IndividualsAssociation)element;
 217                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 218                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 219                     if(tempSpecimenOrObservationBase instanceof DerivedUnitBase){
 220                         try {
 221                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance((DerivedUnitBase)tempSpecimenOrObservationBase));
 222                         } catch (DerivedUnitFacadeNotSupportedException e) {
 223                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 224                         }
 225                     }
 226                 }
 227
 228             }
 229         }
 230
 231         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 232
 233         return derivedUnitFacadeList;
 234     }
 235
 236
 237     /* (non-Javadoc)
 238      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listByAssociatedTaxon(java.lang.Class, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 239      */
 240     @Override
 241     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type,
 242             Taxon associatedTaxon, Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths)
 243     {
 244         return listByAssociatedTaxon(type, null, associatedTaxon, null, limit, start, orderHints, propertyPaths);
 245     }
 246
 247
 248     /* (non-Javadoc)
 249      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listByAnyAssociation(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 250      */
 251     @Override
 252     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 253             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 254
 255         List<Taxon> taxa = new ArrayList<Taxon>();
 256         List<Integer> occurrenceIds = new ArrayList<Integer>();
 257         List<T> occurrences = new ArrayList<T>();
 258
 259
 260         if(includeRelationships != null) {
 261             taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, pageSize, pageSize, propertyPaths);
 262         }
 263
 264         taxa.add((Taxon) taxonDao.load(associatedTaxon.getUuid()));
 265
 266         for (Taxon taxon : taxa) {
 267             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, associatedTaxon, pageSize, pageSize, orderHints, propertyPaths);
 268             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 269                 occurrenceIds.add(o.getId());
 270             }
 271         }
 272
 273         dao.listByIds(occurrenceIds, null, null, orderHints, propertyPaths);
 274
 275         return occurrences;
 276     }
 277
 278
 279     /* (non-Javadoc)
 280      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#pageByAssociatedTaxon(java.lang.Class, java.util.Set, eu.etaxonomy.cdm.model.taxon.Taxon, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
 281      */
 282     @Override
 283     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 284             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 285
 286
 287         return null;
 288     }
 289
 290 }