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.io.IOException;
  14 import java.util.ArrayList;
  15 import java.util.Arrays;
  16 import java.util.HashMap;
  17 import java.util.HashSet;
  18 import java.util.List;
  19 import java.util.Map;
  20 import java.util.Set;
  21
  22 import org.apache.log4j.Logger;
  23 import org.apache.lucene.index.CorruptIndexException;
  24 import org.apache.lucene.queryParser.ParseException;
  25 import org.apache.lucene.search.BooleanClause.Occur;
  26 import org.apache.lucene.search.BooleanQuery;
  27 import org.apache.lucene.search.SortField;
  28 import org.hibernate.search.spatial.impl.Rectangle;
  29 import org.springframework.beans.factory.annotation.Autowired;
  30 import org.springframework.stereotype.Service;
  31 import org.springframework.transaction.annotation.Transactional;
  32
  33 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
  34 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
  35 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
  36 import eu.etaxonomy.cdm.api.service.pager.Pager;
  37 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
  38 import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
  39 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
  40 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
  41 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
  42 import eu.etaxonomy.cdm.api.service.search.QueryFactory;
  43 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  44 import eu.etaxonomy.cdm.api.service.search.SearchResultBuilder;
  45 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  46 import eu.etaxonomy.cdm.common.monitor.IProgressMonitor;
  47 import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
  48 import eu.etaxonomy.cdm.model.CdmBaseType;
  49 import eu.etaxonomy.cdm.model.common.DefinedTermBase;
  50 import eu.etaxonomy.cdm.model.common.Language;
  51 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  52 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  53 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  54 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  55 import eu.etaxonomy.cdm.model.location.Country;
  56 import eu.etaxonomy.cdm.model.media.Media;
  57 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  58 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  59 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  60 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  61 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  62 import eu.etaxonomy.cdm.model.taxon.Taxon;
  63 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  64 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
  65 import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
  66 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
  67 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
  68 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  69 import eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy;
  70
  71 /**
  72  * @author a.babadshanjan
  73  * @created 01.09.2008
  74  */
  75 @Service
  76 @Transactional(readOnly = true)
  77 public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObservationBase,IOccurrenceDao> implements IOccurrenceService {
  78
  79     static private final Logger logger = Logger.getLogger(OccurrenceServiceImpl.class);
  80
  81     @Autowired
  82     private IDefinedTermDao definedTermDao;
  83
  84     @Autowired
  85     private IDescriptionService descriptionService;
  86
  87     @Autowired
  88     private ITaxonService taxonService;
  89
  90     @Autowired
  91     private AbstractBeanInitializer beanInitializer;
  92
  93     @Autowired
  94     private ITaxonDao taxonDao;
  95
  96     @Autowired
  97     private ILuceneIndexToolProvider luceneIndexToolProvider;
  98
  99
 100     public OccurrenceServiceImpl() {
 101         logger.debug("Load OccurrenceService Bean");
 102     }
 103
 104
 105     /* (non-Javadoc)
 106      * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
 107      */
 108     @Override
 109     @Transactional(readOnly = false)
 110     public void updateTitleCache(Class<? extends SpecimenOrObservationBase> clazz, Integer stepSize, IIdentifiableEntityCacheStrategy<SpecimenOrObservationBase> cacheStrategy, IProgressMonitor monitor) {
 111         if (clazz == null){
 112             clazz = SpecimenOrObservationBase.class;
 113         }
 114         super.updateTitleCacheImpl(clazz, stepSize, cacheStrategy, monitor);
 115     }
 116
 117
 118     /**
 119      * FIXME Candidate for harmonization
 120      * move to termService
 121      */
 122     @Override
 123     public Country getCountryByIso(String iso639) {
 124         return this.definedTermDao.getCountryByIso(iso639);
 125
 126     }
 127
 128     /**
 129      * FIXME Candidate for harmonization
 130      * move to termService
 131      */
 132     @Override
 133     public List<Country> getCountryByName(String name) {
 134         List<? extends DefinedTermBase> terms = this.definedTermDao.findByTitle(Country.class, name, null, null, null, null, null, null) ;
 135         List<Country> countries = new ArrayList<Country>();
 136         for (int i=0;i<terms.size();i++){
 137             countries.add((Country)terms.get(i));
 138         }
 139         return countries;
 140     }
 141
 142     @Override
 143     @Autowired
 144     protected void setDao(IOccurrenceDao dao) {
 145         this.dao = dao;
 146     }
 147
 148     @Override
 149     public Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 150         Integer numberOfResults = dao.countDerivationEvents(occurence);
 151
 152         List<DerivationEvent> results = new ArrayList<DerivationEvent>();
 153         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 154             results = dao.getDerivationEvents(occurence, pageSize, pageNumber,propertyPaths);
 155         }
 156
 157         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
 158     }
 159
 160     @Override
 161     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
 162         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
 163
 164         List<DeterminationEvent> results = new ArrayList<DeterminationEvent>();
 165         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 166             results = dao.getDeterminations(occurrence,taxonBase, pageSize, pageNumber, propertyPaths);
 167         }
 168
 169         return new DefaultPagerImpl<DeterminationEvent>(pageNumber, numberOfResults, pageSize, results);
 170     }
 171
 172     @Override
 173     public Pager<Media> getMedia(SpecimenOrObservationBase occurence,Integer pageSize, Integer pageNumber, List<String> propertyPaths) {
 174         Integer numberOfResults = dao.countMedia(occurence);
 175
 176         List<Media> results = new ArrayList<Media>();
 177         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 178             results = dao.getMedia(occurence, pageSize, pageNumber, propertyPaths);
 179         }
 180
 181         return new DefaultPagerImpl<Media>(pageNumber, numberOfResults, pageSize, results);
 182     }
 183
 184     /* (non-Javadoc)
 185      * @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)
 186      */
 187     @Override
 188     public Pager<SpecimenOrObservationBase> list(Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 189         Integer numberOfResults = dao.count(type,determinedAs);
 190         List<SpecimenOrObservationBase> results = new ArrayList<SpecimenOrObservationBase>();
 191         pageNumber = pageNumber == null ? 0 : pageNumber;
 192         if(numberOfResults > 0) { // no point checking again  //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
 193             Integer start = pageSize == null ? 0 : pageSize * pageNumber;
 194             results = dao.list(type,determinedAs, pageSize, start, orderHints,propertyPaths);
 195         }
 196         return new DefaultPagerImpl<SpecimenOrObservationBase>(pageNumber, numberOfResults, pageSize, results);
 197     }
 198
 199     @Override
 200     public List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache() {
 201         return dao.getDerivedUnitUuidAndTitleCache();
 202     }
 203
 204     @Override
 205     public List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache() {
 206         return dao.getFieldUnitUuidAndTitleCache();
 207     }
 208
 209     /* (non-Javadoc)
 210      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
 211      */
 212     @Override
 213     public DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, List<String> propertyPaths) throws DerivedUnitFacadeNotSupportedException {
 214         derivedUnit = (DerivedUnit)dao.load(derivedUnit.getUuid(), null);
 215         DerivedUnitFacadeConfigurator config = DerivedUnitFacadeConfigurator.NewInstance();
 216         config.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
 217         DerivedUnitFacade derivedUnitFacade = DerivedUnitFacade.NewInstance(derivedUnit, config);
 218         beanInitializer.initialize(derivedUnitFacade, propertyPaths);
 219         return derivedUnitFacade;
 220     }
 221
 222     /* (non-Javadoc)
 223      * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
 224      */
 225     @Override
 226     public List<DerivedUnitFacade> listDerivedUnitFacades(
 227             DescriptionBase description, List<String> propertyPaths) {
 228
 229         List<DerivedUnitFacade> derivedUnitFacadeList = new ArrayList<DerivedUnitFacade>();
 230         IndividualsAssociation tempIndividualsAssociation;
 231         SpecimenOrObservationBase tempSpecimenOrObservationBase;
 232         List<DescriptionElementBase> elements = descriptionService.listDescriptionElements(description, null, IndividualsAssociation.class, null, 0, Arrays.asList(new String []{"associatedSpecimenOrObservation"}));
 233         for(DescriptionElementBase element : elements){
 234             if(element instanceof IndividualsAssociation){
 235                 tempIndividualsAssociation = (IndividualsAssociation)element;
 236                 if(tempIndividualsAssociation.getAssociatedSpecimenOrObservation() != null){
 237                     tempSpecimenOrObservationBase = HibernateProxyHelper.deproxy(tempIndividualsAssociation.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase.class);
 238                     if(tempSpecimenOrObservationBase instanceof DerivedUnit){
 239                         try {
 240                             derivedUnitFacadeList.add(DerivedUnitFacade.NewInstance((DerivedUnit)tempSpecimenOrObservationBase));
 241                         } catch (DerivedUnitFacadeNotSupportedException e) {
 242                             logger.warn(tempIndividualsAssociation.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e.getMessage());
 243                         }
 244                     }
 245                 }
 246
 247             }
 248         }
 249
 250         beanInitializer.initializeAll(derivedUnitFacadeList, propertyPaths);
 251
 252         return derivedUnitFacadeList;
 253     }
 254
 255
 256     /* (non-Javadoc)
 257      * @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)
 258      */
 259     @Override
 260     public <T extends SpecimenOrObservationBase> List<T> listByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 261             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 262
 263         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
 264     }
 265
 266
 267     /* (non-Javadoc)
 268      * @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)
 269      */
 270     @SuppressWarnings("unchecked")
 271     @Override
 272     public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
 273             Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
 274
 275         Set<Taxon> taxa = new HashSet<Taxon>();
 276         Set<Integer> occurrenceIds = new HashSet<Integer>();
 277         List<T> occurrences = new ArrayList<T>();
 278
 279 //        Integer limit = PagerUtils.limitFor(pageSize);
 280 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 281
 282         associatedTaxon = (Taxon) taxonDao.load(associatedTaxon.getUuid());
 283
 284         if(includeRelationships != null) {
 285             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
 286         }
 287
 288         taxa.add(associatedTaxon);
 289
 290         for (Taxon taxon : taxa) {
 291             List<T> perTaxonOccurrences = dao.listByAssociatedTaxon(type, taxon, null, null, orderHints, propertyPaths);
 292             for (SpecimenOrObservationBase o : perTaxonOccurrences) {
 293                 occurrenceIds.add(o.getId());
 294             }
 295         }
 296
 297         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 298
 299         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 300
 301     }
 302
 303     @Override
 304     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
 305             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
 306             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 307             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {
 308
 309         LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);
 310
 311         // --- execute search
 312         TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);
 313
 314         Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();
 315         idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");
 316
 317         // --- initialize taxa, highlight matches ....
 318         ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());
 319         @SuppressWarnings("rawtypes")
 320         List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(
 321                 topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);
 322
 323         int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;
 324
 325         return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,
 326                 searchResults);
 327
 328     }
 329
 330
 331     /**
 332      * @param clazz
 333      * @param queryString
 334      * @param languages
 335      * @param highlightFragments
 336      * @return
 337      */
 338     private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,
 339             List<Language> languages, boolean highlightFragments) {
 340
 341         BooleanQuery finalQuery = new BooleanQuery();
 342         BooleanQuery textQuery = new BooleanQuery();
 343
 344         LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
 345         QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 346
 347         // --- criteria
 348         luceneSearch.setCdmTypRestriction(clazz);
 349         if(queryString != null){
 350             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
 351             finalQuery.add(textQuery, Occur.MUST);
 352         }
 353
 354         // --- spacial query
 355         if(bbox != null){
 356             finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);
 357         }
 358
 359         luceneSearch.setQuery(finalQuery);
 360
 361         // --- sorting
 362         SortField[] sortFields = new  SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};
 363         luceneSearch.setSortFields(sortFields);
 364
 365         if(highlightFragments){
 366             luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());
 367         }
 368         return luceneSearch;
 369     }
 370
 371 }