+ /* (non-Javadoc)\r
+ * @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)\r
+ */\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,\r
+ String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {\r
+\r
+ UUID uuid = UUID.fromString(taxonUUID);\r
+ Taxon tax = (Taxon) taxonDao.load(uuid);\r
+ //TODO REMOVE NULL STATEMENT\r
+type=null;\r
+ return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );\r
+\r
+ }\r
+\r
+\r
+ @Override\r
+ public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(\r
+ Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,\r
+ boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,\r
+ List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException {\r
+\r
+ LuceneSearch luceneSearch = prepareByFullTextSearch(clazz, queryString, boundingBox, languages, highlightFragments);\r
+\r
+ // --- execute search\r
+ TopGroupsWithMaxScore topDocsResultSet = luceneSearch.executeSearch(pageSize, pageNumber);\r
+\r
+ Map<CdmBaseType, String> idFieldMap = new HashMap<CdmBaseType, String>();\r
+ idFieldMap.put(CdmBaseType.SPECIMEN_OR_OBSERVATIONBASE, "id");\r
+\r
+ // --- initialize taxa, highlight matches ....\r
+ ISearchResultBuilder searchResultBuilder = new SearchResultBuilder(luceneSearch, luceneSearch.getQuery());\r
+ @SuppressWarnings("rawtypes")\r
+ List<SearchResult<SpecimenOrObservationBase>> searchResults = searchResultBuilder.createResultSet(\r
+ topDocsResultSet, luceneSearch.getHighlightFields(), dao, idFieldMap, propertyPaths);\r
+\r
+ int totalHits = topDocsResultSet != null ? topDocsResultSet.topGroups.totalGroupCount : 0;\r
+\r
+ return new DefaultPagerImpl<SearchResult<SpecimenOrObservationBase>>(pageNumber, totalHits, pageSize,\r
+ searchResults);\r
+\r
+ }\r
+\r
+\r
+ /**\r
+ * @param clazz\r
+ * @param queryString\r
+ * @param languages\r
+ * @param highlightFragments\r
+ * @return\r
+ */\r
+ private LuceneSearch prepareByFullTextSearch(Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle bbox,\r
+ List<Language> languages, boolean highlightFragments) {\r
+\r
+ BooleanQuery finalQuery = new BooleanQuery();\r
+ BooleanQuery textQuery = new BooleanQuery();\r
+\r
+ LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);\r
+ QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);\r
+\r
+ // --- criteria\r
+ luceneSearch.setCdmTypRestriction(clazz);\r
+ if(queryString != null){\r
+ textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);\r
+ finalQuery.add(textQuery, Occur.MUST);\r
+ }\r
+\r
+ // --- spacial query\r
+ if(bbox != null){\r
+ finalQuery.add(QueryFactory.buildSpatialQueryByRange(bbox, "gatheringEvent.exactLocation.point"), Occur.MUST);\r
+ }\r
+\r
+ luceneSearch.setQuery(finalQuery);\r
+\r
+ // --- sorting\r
+ SortField[] sortFields = new SortField[]{SortField.FIELD_SCORE, new SortField("titleCache__sort", SortField.STRING, false)};\r
+ luceneSearch.setSortFields(sortFields);\r
+\r
+ if(highlightFragments){\r
+ luceneSearch.setHighlightFields(queryFactory.getTextFieldNamesAsArray());\r
+ }\r
+ return luceneSearch;\r
+ }\r
+\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)\r
+ */\r
+ @Override\r
+ public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {\r
+ //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})\r
+ //from which this DerivedUnit was derived until all FieldUnits are found.\r
+\r
+ //FIXME: use HQL queries to increase performance\r
+ SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);\r
+// specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);\r
+ Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();\r
+\r
+ if(specimen instanceof FieldUnit){\r
+ fieldUnits.add((FieldUnit) specimen);\r
+ }\r
+ else if(specimen instanceof DerivedUnit){\r
+ getFieldUnits((DerivedUnit) specimen, fieldUnits);\r
+ }\r
+ return fieldUnits;\r
+ }\r
+\r
+\r
+ /**\r
+ * @param original\r
+ * @param fieldUnits\r
+ */\r
+ private void getFieldUnits(DerivedUnit derivedUnit, Collection<FieldUnit> fieldUnits) {\r
+ Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();\r
+ if(originals!=null && !originals.isEmpty()){\r
+ for(SpecimenOrObservationBase<?> original:originals){\r
+ if(original instanceof FieldUnit){\r
+ fieldUnits.add((FieldUnit) original);\r
+ }\r
+ else if(original instanceof DerivedUnit){\r
+ getFieldUnits((DerivedUnit) original, fieldUnits);\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#moveSequence(eu.etaxonomy.cdm.model.molecular.DnaSample, eu.etaxonomy.cdm.model.molecular.DnaSample, eu.etaxonomy.cdm.model.molecular.Sequence)\r
+ */\r
+ @Override\r
+ public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {\r
+ //reload specimens to avoid session conflicts\r
+ from = (DnaSample) load(from.getUuid());\r
+ to = (DnaSample) load(to.getUuid());\r
+ sequence = sequenceService.load(sequence.getUuid());\r
+\r
+ if(from==null || to==null || sequence==null){\r
+ throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +\r
+ "Operation was move "+sequence+ " from "+from+" to "+to);\r
+ }\r
+ from.removeSequence(sequence);\r
+ saveOrUpdate(from);\r
+ to.addSequence(sequence);\r
+ saveOrUpdate(to);\r
+ return true;\r
+ }\r
+\r
+ /* (non-Javadoc)\r
+ * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#moveDerivate(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.occurrence.DerivedUnit)\r
+ */\r
+ @Override\r
+ public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {\r
+ //reload specimens to avoid session conflicts\r
+ from = load(from.getUuid());\r
+ to = load(to.getUuid());\r
+ derivate = (DerivedUnit) load(derivate.getUuid());\r
+\r
+ if(from==null || to==null || derivate==null){\r
+ throw new TransientObjectException("One of the CDM entities has not been saved to the data base yet. Moving only works for persisted/saved CDM entities.\n" +\r
+ "Operation was move "+derivate+ " from "+from+" to "+to);\r
+ }\r
+\r
+ SpecimenOrObservationType derivateType = derivate.getRecordBasis();\r
+ SpecimenOrObservationType toType = to.getRecordBasis();\r
+ //check if type is a sub derivate type\r
+ if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works\r
+ || derivateType==SpecimenOrObservationType.Media //moving media always works\r
+ || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type\r
+ //remove derivation event from parent specimen of dragged object\r
+ DerivationEvent eventToRemove = null;\r
+ for(DerivationEvent event:from.getDerivationEvents()){\r
+ if(event.getDerivatives().contains(derivate)){\r
+ eventToRemove = event;\r
+ break;\r
+ }\r
+ }\r
+ from.removeDerivationEvent(eventToRemove);\r
+ saveOrUpdate(from);\r
+ //add new derivation event to target\r
+ to.addDerivationEvent(DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType()));\r
+ saveOrUpdate(to);\r
+ return true;\r
+ }\r
+ return false;\r
+ }\r
+\r