X-Git-Url: https://dev.e-taxonomy.eu/gitweb/cdmlib.git/blobdiff_plain/199ed72a78b464290b2470e7f5dc823a1373d6aa..ad80fdc31885697feed8d22235415bedff69c30b:/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java

diff --git a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
index 1aa70ce295..2cd090df46 100644
--- a/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
+++ b/cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceImpl.java
@@ -13,11 +13,14 @@ package eu.etaxonomy.cdm.api.service;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collection;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
+import java.util.UUID;
 
 import org.apache.log4j.Logger;
 import org.apache.lucene.index.CorruptIndexException;
@@ -25,6 +28,7 @@ import org.apache.lucene.queryParser.ParseException;
 import org.apache.lucene.search.BooleanClause.Occur;
 import org.apache.lucene.search.BooleanQuery;
 import org.apache.lucene.search.SortField;
+import org.hibernate.TransientObjectException;
 import org.hibernate.search.spatial.impl.Rectangle;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
@@ -33,8 +37,11 @@ import org.springframework.transaction.annotation.Transactional;
 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacade;
 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeConfigurator;
 import eu.etaxonomy.cdm.api.facade.DerivedUnitFacadeNotSupportedException;
+import eu.etaxonomy.cdm.api.service.dto.DerivateHierarchyDTO;
+import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
 import eu.etaxonomy.cdm.api.service.pager.Pager;
 import eu.etaxonomy.cdm.api.service.pager.impl.DefaultPagerImpl;
+import eu.etaxonomy.cdm.api.service.search.ILuceneIndexToolProvider;
 import eu.etaxonomy.cdm.api.service.search.ISearchResultBuilder;
 import eu.etaxonomy.cdm.api.service.search.LuceneSearch;
 import eu.etaxonomy.cdm.api.service.search.LuceneSearch.TopGroupsWithMaxScore;
@@ -53,15 +60,22 @@ import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
 import eu.etaxonomy.cdm.model.location.Country;
 import eu.etaxonomy.cdm.model.media.Media;
+import eu.etaxonomy.cdm.model.media.MediaRepresentation;
+import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;
+import eu.etaxonomy.cdm.model.molecular.DnaSample;
+import eu.etaxonomy.cdm.model.molecular.Sequence;
 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
+import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
+import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
+import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 import eu.etaxonomy.cdm.model.taxon.Taxon;
 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
-import eu.etaxonomy.cdm.persistence.dao.AbstractBeanInitializer;
 import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
+import eu.etaxonomy.cdm.persistence.dao.initializer.AbstractBeanInitializer;
 import eu.etaxonomy.cdm.persistence.dao.occurrence.IOccurrenceDao;
 import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
 import eu.etaxonomy.cdm.persistence.query.OrderHint;
@@ -86,12 +100,17 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
     @Autowired
     private ITaxonService taxonService;
 
+    @Autowired
+    private ISequenceService sequenceService;
+
     @Autowired
     private AbstractBeanInitializer beanInitializer;
 
     @Autowired
     private ITaxonDao taxonDao;
 
+    @Autowired
+    private ILuceneIndexToolProvider luceneIndexToolProvider;
 
 
     public OccurrenceServiceImpl() {
@@ -154,6 +173,14 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
         return new DefaultPagerImpl<DerivationEvent>(pageNumber, numberOfResults, pageSize, results);
     }
 
+    /* (non-Javadoc)
+     * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
+     */
+    @Override
+    public int countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase) {
+        return dao.countDeterminations(occurence, taxonbase);
+    }
+
     @Override
     public Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurrence, TaxonBase taxonBase, Integer pageSize,Integer pageNumber, List<String> propertyPaths) {
         Integer numberOfResults = dao.countDeterminations(occurrence, taxonBase);
@@ -260,6 +287,162 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
         return pageByAssociatedTaxon(type, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
     }
 
+    /* (non-Javadoc)
+     * @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)
+     */
+    @Override
+    public Collection<FieldUnit> listFieldUnitsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
+            Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+
+        if(!getSession().contains(associatedTaxon)){
+            associatedTaxon = (Taxon) taxonDao.load(associatedTaxon.getUuid());
+        }
+
+        Set<FieldUnit> fieldUnits = new HashSet<FieldUnit>();
+
+        List<SpecimenOrObservationBase> records = pageByAssociatedTaxon(null, includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths).getRecords();
+        for(SpecimenOrObservationBase<?> specimen:records){
+            fieldUnits.addAll(getFieldUnits(specimen.getUuid()));
+        }
+        return fieldUnits;
+    }
+
+    @Override
+    public Collection<DerivateHierarchyDTO> listDerivateHierarchyDTOsByAssociatedTaxon(Set<TaxonRelationshipEdge> includeRelationships,
+            Taxon associatedTaxon, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+
+        if(!getSession().contains(associatedTaxon)){
+            associatedTaxon = (Taxon) taxonDao.load(associatedTaxon.getUuid());
+        }
+
+        Collection<FieldUnit> fieldUnits = listFieldUnitsByAssociatedTaxon(includeRelationships, associatedTaxon, maxDepth, pageSize, pageNumber, orderHints, propertyPaths);
+
+        Collection<DerivateHierarchyDTO> derivateHierarchyDTOs = new ArrayList<DerivateHierarchyDTO>();
+        for(FieldUnit fieldUnit:fieldUnits){
+            derivateHierarchyDTOs.add(assembleDerivateHierarchyDTO(fieldUnit, associatedTaxon));
+        }
+        return derivateHierarchyDTOs;
+    }
+
+    private DerivateHierarchyDTO assembleDerivateHierarchyDTO(FieldUnit fieldUnit, Taxon associatedTaxon){
+
+        DerivateHierarchyDTO dto = new DerivateHierarchyDTO();
+        //        TaxonNameBase name = associatedTaxon.getName();
+        //        name = HibernateProxyHelper.deproxy(name, TaxonNameBase.class);
+        //        dto.setType(!name.getTypeDesignations().isEmpty());
+
+        if(fieldUnit.getGatheringEvent()!=null){
+            GatheringEvent gatheringEvent = fieldUnit.getGatheringEvent();
+            //Country
+            dto.setCountry(gatheringEvent.getCountry()!=null?gatheringEvent.getCountry().getDescription():"");
+            //Collection
+            dto.setCollection((gatheringEvent.getCollector()!=null?gatheringEvent.getCollector():"") + fieldUnit.getFieldNumber()!=null?fieldUnit.getFieldNumber():"");
+            //Date
+            dto.setDate(gatheringEvent.getGatheringDate()!=null?gatheringEvent.getGatheringDate().toString():"");
+        }
+
+        //Taxon Name
+        dto.setTaxonName(associatedTaxon.getName().getFullTitleCache());
+
+
+        Collection<DerivedUnit> derivedUnits = new ArrayList<DerivedUnit>();
+        getDerivedUnitsFor(fieldUnit, derivedUnits);
+        //Herbaria map
+        Map<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> collectionToCountMap = new HashMap<eu.etaxonomy.cdm.model.occurrence.Collection, Integer>();
+
+        //iterate over sub derivates
+        for (DerivedUnit derivedUnit : derivedUnits) {
+            //assemble molecular data
+            if(derivedUnit instanceof DnaSample){//.getRecordBasis()==SpecimenOrObservationType.DnaSample){
+                dto.setHasDna(true);
+
+                DnaSample dna = (DnaSample)derivedUnit;
+                if(dna.getBankNumber()!=null){
+                    dto.addMolecularData(dna.getBankNumber());
+                }
+            }
+            //assemble media data
+            else if(derivedUnit instanceof MediaSpecimen){
+
+                MediaSpecimen media = (MediaSpecimen)derivedUnit;
+                String mediaUriString = getMediaUriString(media);
+                if(media.getKindOfUnit()!=null){
+                    if(media.getKindOfUnit().getUuid().equals(UUID.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
+                        dto.setHasSpecimenScan(true);
+                        if(mediaUriString!=null){
+                            dto.addSpecimenScan(mediaUriString);
+                        }
+                    }
+                    else if(media.getKindOfUnit().getUuid().equals(UUID.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
+                        dto.setHasDetailImage(true);
+                        if(mediaUriString!=null){
+                            dto.addDetailImage(mediaUriString);
+                        }
+                    }
+                }
+            }
+            //assemble preserved specimen data
+            else if(derivedUnit.getRecordBasis()==SpecimenOrObservationType.PreservedSpecimen){
+                eu.etaxonomy.cdm.model.occurrence.Collection collection = derivedUnit.getCollection();
+                if(collection!=null){
+                    Integer count = collectionToCountMap.get(collection);
+                    if(count==null){
+                        count = 1;
+                    }
+                    else{
+                        count++;
+                    }
+                    collectionToCountMap.put(collection, count);
+                }
+            }
+        }
+        //assemble herbaria string
+        String herbariaString = "";
+        final String herbariaSeparator = ", ";
+        for(Entry<eu.etaxonomy.cdm.model.occurrence.Collection, Integer> e:collectionToCountMap.entrySet()){
+            eu.etaxonomy.cdm.model.occurrence.Collection collection = e.getKey();
+            if(collection.getCode()!=null){
+                herbariaString += collection.getCode();
+            }
+            if(e.getValue()>1){
+                herbariaString += "("+e.getValue()+")";
+            }
+            herbariaString += herbariaSeparator;
+        }
+        if(herbariaString.endsWith(herbariaSeparator)){
+            herbariaString = herbariaString.substring(0, herbariaString.length()-herbariaSeparator.length());
+        }
+        dto.setHerbarium(herbariaString);
+        return dto;
+    }
+
+    private String getMediaUriString(MediaSpecimen mediaSpecimen){
+        if(!getSession().contains(mediaSpecimen)){
+            mediaSpecimen = (MediaSpecimen) load(mediaSpecimen.getUuid());
+        }
+        String mediaUri = null;
+        Collection<MediaRepresentation> mediaRepresentations = mediaSpecimen.getMediaSpecimen().getRepresentations();
+        if(mediaRepresentations!=null && !mediaRepresentations.isEmpty()){
+            Collection<MediaRepresentationPart> mediaRepresentationParts = mediaRepresentations.iterator().next().getParts();
+            if(mediaRepresentationParts!=null && !mediaRepresentationParts.isEmpty()){
+                MediaRepresentationPart part = mediaRepresentationParts.iterator().next();
+                if(part.getUri()!=null){
+                    mediaUri = part.getUri().toASCIIString();
+                }
+            }
+        }
+        return mediaUri;
+    }
+
+    private void getDerivedUnitsFor(SpecimenOrObservationBase<?> specimen, Collection<DerivedUnit> derivedUnits){
+        for(DerivationEvent derivationEvent:specimen.getDerivationEvents()){
+            for(DerivedUnit derivative:derivationEvent.getDerivatives()){
+                derivedUnits.add(derivative);
+                getDerivedUnitsFor(derivative, derivedUnits);
+            }
+        }
+    }
+
 
     /* (non-Javadoc)
      * @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)
@@ -276,7 +459,9 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
 //        Integer limit = PagerUtils.limitFor(pageSize);
 //        Integer start = PagerUtils.startFor(pageSize, pageNumber);
 
-        associatedTaxon = (Taxon) taxonDao.load(associatedTaxon.getUuid());
+        if(!getSession().contains(associatedTaxon)){
+            associatedTaxon = (Taxon) taxonDao.load(associatedTaxon.getUuid());
+        }
 
         if(includeRelationships != null) {
             taxa = taxonService.listRelatedTaxa(associatedTaxon, includeRelationships, maxDepth, null, null, propertyPaths);
@@ -290,13 +475,29 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
                 occurrenceIds.add(o.getId());
             }
         }
-
         occurrences = (List<T>) dao.listByIds(occurrenceIds, pageSize, pageNumber, orderHints, propertyPaths);
 
         return new DefaultPagerImpl<T>(pageNumber, occurrenceIds.size(), pageSize, occurrences);
 
     }
 
+    /* (non-Javadoc)
+     * @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)
+     */
+    @SuppressWarnings("unchecked")
+    @Override
+    public <T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(Class<T> type, Set<TaxonRelationshipEdge> includeRelationships,
+            String taxonUUID, Integer maxDepth, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) {
+
+        UUID uuid = UUID.fromString(taxonUUID);
+        Taxon tax = (Taxon) taxonDao.load(uuid);
+       //TODO REMOVE NULL STATEMENT
+type=null;
+        return pageByAssociatedTaxon( type,includeRelationships,tax, maxDepth, pageSize, pageNumber, orderHints, propertyPaths );
+
+    }
+
+
     @Override
     public Pager<SearchResult<SpecimenOrObservationBase>> findByFullText(
             Class<? extends SpecimenOrObservationBase> clazz, String queryString, Rectangle boundingBox, List<Language> languages,
@@ -338,11 +539,11 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
         BooleanQuery finalQuery = new BooleanQuery();
         BooleanQuery textQuery = new BooleanQuery();
 
-        LuceneSearch luceneSearch = new LuceneSearch(getSession(), FieldUnit.class);
-        QueryFactory queryFactory = new QueryFactory(luceneSearch);
+        LuceneSearch luceneSearch = new LuceneSearch(luceneIndexToolProvider, FieldUnit.class);
+        QueryFactory queryFactory = luceneIndexToolProvider.newQueryFactoryFor(FieldUnit.class);
 
         // --- criteria
-        luceneSearch.setClazz(clazz);
+        luceneSearch.setCdmTypRestriction(clazz);
         if(queryString != null){
             textQuery.add(queryFactory.newTermQuery("titleCache", queryString), Occur.SHOULD);
             finalQuery.add(textQuery, Occur.MUST);
@@ -365,4 +566,106 @@ public class OccurrenceServiceImpl extends IdentifiableServiceBase<SpecimenOrObs
         return luceneSearch;
     }
 
+
+    /* (non-Javadoc)
+     * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
+     */
+    @Override
+    public Collection<FieldUnit> getFieldUnits(UUID derivedUnitUuid) {
+        //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
+        //from which this DerivedUnit was derived until all FieldUnits are found.
+
+        //FIXME: use HQL queries to increase performance
+        SpecimenOrObservationBase<?> specimen = load(derivedUnitUuid);
+//        specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
+        Collection<FieldUnit> fieldUnits = new ArrayList<FieldUnit>();
+
+        if(specimen instanceof FieldUnit){
+            fieldUnits.add((FieldUnit) specimen);
+        }
+        else if(specimen instanceof DerivedUnit){
+            getFieldUnits((DerivedUnit) specimen, fieldUnits);
+        }
+        return fieldUnits;
+    }
+
+
+    /**
+     * @param original
+     * @param fieldUnits
+     */
+    private void getFieldUnits(DerivedUnit derivedUnit, Collection<FieldUnit> fieldUnits) {
+        Set<SpecimenOrObservationBase> originals = derivedUnit.getOriginals();
+        if(originals!=null && !originals.isEmpty()){
+            for(SpecimenOrObservationBase<?> original:originals){
+                if(original instanceof FieldUnit){
+                    fieldUnits.add((FieldUnit) original);
+                }
+                else if(original instanceof DerivedUnit){
+                    getFieldUnits((DerivedUnit) original, fieldUnits);
+                }
+            }
+        }
+    }
+
+    /* (non-Javadoc)
+     * @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)
+     */
+    @Override
+    public boolean moveSequence(DnaSample from, DnaSample to, Sequence sequence) {
+        //reload specimens to avoid session conflicts
+        from = (DnaSample) load(from.getUuid());
+        to = (DnaSample) load(to.getUuid());
+        sequence = sequenceService.load(sequence.getUuid());
+
+        if(from==null || to==null || sequence==null){
+            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" +
+                    "Operation was move "+sequence+ " from "+from+" to "+to);
+        }
+        from.removeSequence(sequence);
+        saveOrUpdate(from);
+        to.addSequence(sequence);
+        saveOrUpdate(to);
+        return true;
+    }
+
+    /* (non-Javadoc)
+     * @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)
+     */
+    @Override
+    public boolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate) {
+        //reload specimens to avoid session conflicts
+        from = load(from.getUuid());
+        to = load(to.getUuid());
+        derivate = (DerivedUnit) load(derivate.getUuid());
+
+        if(from==null || to==null || derivate==null){
+            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" +
+            		"Operation was move "+derivate+ " from "+from+" to "+to);
+        }
+
+        SpecimenOrObservationType derivateType = derivate.getRecordBasis();
+        SpecimenOrObservationType toType = to.getRecordBasis();
+        //check if type is a sub derivate type
+        if(toType==SpecimenOrObservationType.FieldUnit //moving to FieldUnit always works
+                || derivateType==SpecimenOrObservationType.Media //moving media always works
+                || (derivateType.isKindOf(toType) && toType!=derivateType)){ //moving only to parent derivate type
+            //remove derivation event from parent specimen of dragged object
+            DerivationEvent eventToRemove = null;
+            for(DerivationEvent event:from.getDerivationEvents()){
+                if(event.getDerivatives().contains(derivate)){
+                    eventToRemove = event;
+                    break;
+                }
+            }
+            from.removeDerivationEvent(eventToRemove);
+            saveOrUpdate(from);
+            //add new derivation event to target
+            to.addDerivationEvent(DerivationEvent.NewSimpleInstance(to, derivate, eventToRemove==null?null:eventToRemove.getType()));
+            saveOrUpdate(to);
+            return true;
+        }
+        return false;
+    }
+
 }