3 * Copyright (C) 2007 EDIT
4 * European Distributed Institute of Taxonomy
5 * http://www.e-taxonomy.eu
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.
11 package eu
.etaxonomy
.cdm
.api
.service
;
13 import java
.io
.IOException
;
15 import java
.util
.ArrayList
;
16 import java
.util
.Arrays
;
17 import java
.util
.Collection
;
18 import java
.util
.HashMap
;
19 import java
.util
.HashSet
;
20 import java
.util
.List
;
22 import java
.util
.Map
.Entry
;
24 import java
.util
.UUID
;
26 import org
.apache
.log4j
.Logger
;
27 import org
.apache
.lucene
.index
.CorruptIndexException
;
28 import org
.apache
.lucene
.queryParser
.ParseException
;
29 import org
.apache
.lucene
.search
.BooleanClause
.Occur
;
30 import org
.apache
.lucene
.search
.BooleanQuery
;
31 import org
.apache
.lucene
.search
.SortField
;
32 import org
.hibernate
.TransientObjectException
;
33 import org
.hibernate
.search
.spatial
.impl
.Rectangle
;
34 import org
.joda
.time
.Partial
;
35 import org
.springframework
.beans
.factory
.annotation
.Autowired
;
36 import org
.springframework
.stereotype
.Service
;
37 import org
.springframework
.transaction
.annotation
.Transactional
;
39 import eu
.etaxonomy
.cdm
.api
.facade
.DerivedUnitFacade
;
40 import eu
.etaxonomy
.cdm
.api
.facade
.DerivedUnitFacadeConfigurator
;
41 import eu
.etaxonomy
.cdm
.api
.facade
.DerivedUnitFacadeNotSupportedException
;
42 import eu
.etaxonomy
.cdm
.api
.service
.dto
.DerivateHierarchyDTO
;
43 import eu
.etaxonomy
.cdm
.api
.service
.molecular
.ISequenceService
;
44 import eu
.etaxonomy
.cdm
.api
.service
.pager
.Pager
;
45 import eu
.etaxonomy
.cdm
.api
.service
.pager
.impl
.DefaultPagerImpl
;
46 import eu
.etaxonomy
.cdm
.api
.service
.search
.ILuceneIndexToolProvider
;
47 import eu
.etaxonomy
.cdm
.api
.service
.search
.ISearchResultBuilder
;
48 import eu
.etaxonomy
.cdm
.api
.service
.search
.LuceneSearch
;
49 import eu
.etaxonomy
.cdm
.api
.service
.search
.LuceneSearch
.TopGroupsWithMaxScore
;
50 import eu
.etaxonomy
.cdm
.api
.service
.search
.QueryFactory
;
51 import eu
.etaxonomy
.cdm
.api
.service
.search
.SearchResult
;
52 import eu
.etaxonomy
.cdm
.api
.service
.search
.SearchResultBuilder
;
53 import eu
.etaxonomy
.cdm
.api
.service
.util
.TaxonRelationshipEdge
;
54 import eu
.etaxonomy
.cdm
.common
.monitor
.IProgressMonitor
;
55 import eu
.etaxonomy
.cdm
.hibernate
.HibernateProxyHelper
;
56 import eu
.etaxonomy
.cdm
.model
.CdmBaseType
;
57 import eu
.etaxonomy
.cdm
.model
.agent
.AgentBase
;
58 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTerm
;
59 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTermBase
;
60 import eu
.etaxonomy
.cdm
.model
.common
.ICdmBase
;
61 import eu
.etaxonomy
.cdm
.model
.common
.Language
;
62 import eu
.etaxonomy
.cdm
.model
.common
.UuidAndTitleCache
;
63 import eu
.etaxonomy
.cdm
.model
.description
.DescriptionBase
;
64 import eu
.etaxonomy
.cdm
.model
.description
.DescriptionElementBase
;
65 import eu
.etaxonomy
.cdm
.model
.description
.IndividualsAssociation
;
66 import eu
.etaxonomy
.cdm
.model
.location
.Country
;
67 import eu
.etaxonomy
.cdm
.model
.location
.NamedArea
;
68 import eu
.etaxonomy
.cdm
.model
.media
.Media
;
69 import eu
.etaxonomy
.cdm
.model
.media
.MediaRepresentation
;
70 import eu
.etaxonomy
.cdm
.model
.media
.MediaRepresentationPart
;
71 import eu
.etaxonomy
.cdm
.model
.molecular
.DnaSample
;
72 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
73 import eu
.etaxonomy
.cdm
.model
.name
.SpecimenTypeDesignation
;
74 import eu
.etaxonomy
.cdm
.model
.name
.TaxonNameBase
;
75 import eu
.etaxonomy
.cdm
.model
.name
.TypeDesignationStatusBase
;
76 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivationEvent
;
77 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivedUnit
;
78 import eu
.etaxonomy
.cdm
.model
.occurrence
.DeterminationEvent
;
79 import eu
.etaxonomy
.cdm
.model
.occurrence
.FieldUnit
;
80 import eu
.etaxonomy
.cdm
.model
.occurrence
.GatheringEvent
;
81 import eu
.etaxonomy
.cdm
.model
.occurrence
.MediaSpecimen
;
82 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationBase
;
83 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationType
;
84 import eu
.etaxonomy
.cdm
.model
.taxon
.Taxon
;
85 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonBase
;
86 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.IDefinedTermDao
;
87 import eu
.etaxonomy
.cdm
.persistence
.dao
.initializer
.AbstractBeanInitializer
;
88 import eu
.etaxonomy
.cdm
.persistence
.dao
.occurrence
.IOccurrenceDao
;
89 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
;
90 import eu
.etaxonomy
.cdm
.strategy
.cache
.common
.IIdentifiableEntityCacheStrategy
;
93 * @author a.babadshanjan
97 @Transactional(readOnly
= true)
98 public class OccurrenceServiceImpl
extends IdentifiableServiceBase
<SpecimenOrObservationBase
,IOccurrenceDao
> implements IOccurrenceService
{
100 static private final Logger logger
= Logger
.getLogger(OccurrenceServiceImpl
.class);
103 private IDefinedTermDao definedTermDao
;
106 private IDescriptionService descriptionService
;
109 private ITaxonService taxonService
;
112 private ITermService termService
;
115 private INameService nameService
;
118 private ISequenceService sequenceService
;
121 private AbstractBeanInitializer beanInitializer
;
124 private ILuceneIndexToolProvider luceneIndexToolProvider
;
127 public OccurrenceServiceImpl() {
128 logger
.debug("Load OccurrenceService Bean");
133 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy)
136 @Transactional(readOnly
= false)
137 public void updateTitleCache(Class
<?
extends SpecimenOrObservationBase
> clazz
, Integer stepSize
, IIdentifiableEntityCacheStrategy
<SpecimenOrObservationBase
> cacheStrategy
, IProgressMonitor monitor
) {
139 clazz
= SpecimenOrObservationBase
.class;
141 super.updateTitleCacheImpl(clazz
, stepSize
, cacheStrategy
, monitor
);
146 * FIXME Candidate for harmonization
147 * move to termService
150 public Country
getCountryByIso(String iso639
) {
151 return this.definedTermDao
.getCountryByIso(iso639
);
156 * FIXME Candidate for harmonization
157 * move to termService
160 public List
<Country
> getCountryByName(String name
) {
161 List
<?
extends DefinedTermBase
> terms
= this.definedTermDao
.findByTitle(Country
.class, name
, null, null, null, null, null, null) ;
162 List
<Country
> countries
= new ArrayList
<Country
>();
163 for (int i
=0;i
<terms
.size();i
++){
164 countries
.add((Country
)terms
.get(i
));
171 protected void setDao(IOccurrenceDao dao
) {
176 public Pager
<DerivationEvent
> getDerivationEvents(SpecimenOrObservationBase occurence
, Integer pageSize
,Integer pageNumber
, List
<String
> propertyPaths
) {
177 Integer numberOfResults
= dao
.countDerivationEvents(occurence
);
179 List
<DerivationEvent
> results
= new ArrayList
<DerivationEvent
>();
180 if(numberOfResults
> 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
181 results
= dao
.getDerivationEvents(occurence
, pageSize
, pageNumber
,propertyPaths
);
184 return new DefaultPagerImpl
<DerivationEvent
>(pageNumber
, numberOfResults
, pageSize
, results
);
188 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
191 public int countDeterminations(SpecimenOrObservationBase occurence
, TaxonBase taxonbase
) {
192 return dao
.countDeterminations(occurence
, taxonbase
);
196 public Pager
<DeterminationEvent
> getDeterminations(SpecimenOrObservationBase occurrence
, TaxonBase taxonBase
, Integer pageSize
,Integer pageNumber
, List
<String
> propertyPaths
) {
197 Integer numberOfResults
= dao
.countDeterminations(occurrence
, taxonBase
);
199 List
<DeterminationEvent
> results
= new ArrayList
<DeterminationEvent
>();
200 if(numberOfResults
> 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
201 results
= dao
.getDeterminations(occurrence
,taxonBase
, pageSize
, pageNumber
, propertyPaths
);
204 return new DefaultPagerImpl
<DeterminationEvent
>(pageNumber
, numberOfResults
, pageSize
, results
);
208 public Pager
<Media
> getMedia(SpecimenOrObservationBase occurence
,Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
209 Integer numberOfResults
= dao
.countMedia(occurence
);
211 List
<Media
> results
= new ArrayList
<Media
>();
212 if(numberOfResults
> 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
213 results
= dao
.getMedia(occurence
, pageSize
, pageNumber
, propertyPaths
);
216 return new DefaultPagerImpl
<Media
>(pageNumber
, numberOfResults
, pageSize
, results
);
220 * @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)
223 public Pager
<SpecimenOrObservationBase
> list(Class
<?
extends SpecimenOrObservationBase
> type
, TaxonBase determinedAs
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
224 Integer numberOfResults
= dao
.count(type
,determinedAs
);
225 List
<SpecimenOrObservationBase
> results
= new ArrayList
<SpecimenOrObservationBase
>();
226 pageNumber
= pageNumber
== null ?
0 : pageNumber
;
227 if(numberOfResults
> 0) { // no point checking again //TODO use AbstractPagerImpl.hasResultsInRange(numberOfResults, pageNumber, pageSize)
228 Integer start
= pageSize
== null ?
0 : pageSize
* pageNumber
;
229 results
= dao
.list(type
,determinedAs
, pageSize
, start
, orderHints
,propertyPaths
);
231 return new DefaultPagerImpl
<SpecimenOrObservationBase
>(pageNumber
, numberOfResults
, pageSize
, results
);
235 public List
<UuidAndTitleCache
<DerivedUnit
>> getDerivedUnitUuidAndTitleCache() {
236 return dao
.getDerivedUnitUuidAndTitleCache();
240 public List
<UuidAndTitleCache
<FieldUnit
>> getFieldUnitUuidAndTitleCache() {
241 return dao
.getFieldUnitUuidAndTitleCache();
245 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
248 public DerivedUnitFacade
getDerivedUnitFacade(DerivedUnit derivedUnit
, List
<String
> propertyPaths
) throws DerivedUnitFacadeNotSupportedException
{
249 derivedUnit
= (DerivedUnit
)dao
.load(derivedUnit
.getUuid(), null);
250 DerivedUnitFacadeConfigurator config
= DerivedUnitFacadeConfigurator
.NewInstance();
251 config
.setThrowExceptionForNonSpecimenPreservationMethodRequest(false);
252 DerivedUnitFacade derivedUnitFacade
= DerivedUnitFacade
.NewInstance(derivedUnit
, config
);
253 beanInitializer
.initialize(derivedUnitFacade
, propertyPaths
);
254 return derivedUnitFacade
;
258 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
261 public List
<DerivedUnitFacade
> listDerivedUnitFacades(
262 DescriptionBase description
, List
<String
> propertyPaths
) {
264 List
<DerivedUnitFacade
> derivedUnitFacadeList
= new ArrayList
<DerivedUnitFacade
>();
265 IndividualsAssociation tempIndividualsAssociation
;
266 SpecimenOrObservationBase tempSpecimenOrObservationBase
;
267 List
<DescriptionElementBase
> elements
= descriptionService
.listDescriptionElements(description
, null, IndividualsAssociation
.class, null, 0, Arrays
.asList(new String
[]{"associatedSpecimenOrObservation"}));
268 for(DescriptionElementBase element
: elements
){
269 if(element
instanceof IndividualsAssociation
){
270 tempIndividualsAssociation
= (IndividualsAssociation
)element
;
271 if(tempIndividualsAssociation
.getAssociatedSpecimenOrObservation() != null){
272 tempSpecimenOrObservationBase
= HibernateProxyHelper
.deproxy(tempIndividualsAssociation
.getAssociatedSpecimenOrObservation(), SpecimenOrObservationBase
.class);
273 if(tempSpecimenOrObservationBase
instanceof DerivedUnit
){
275 derivedUnitFacadeList
.add(DerivedUnitFacade
.NewInstance((DerivedUnit
)tempSpecimenOrObservationBase
));
276 } catch (DerivedUnitFacadeNotSupportedException e
) {
277 logger
.warn(tempIndividualsAssociation
.getAssociatedSpecimenOrObservation().getTitleCache() + " : " +e
.getMessage());
285 beanInitializer
.initializeAll(derivedUnitFacadeList
, propertyPaths
);
287 return derivedUnitFacadeList
;
292 * @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)
295 public <T
extends SpecimenOrObservationBase
> List
<T
> listByAssociatedTaxon(Class
<T
> type
, Set
<TaxonRelationshipEdge
> includeRelationships
,
296 Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
298 return pageByAssociatedTaxon(type
, includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
).getRecords();
302 * @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)
305 public Collection
<FieldUnit
> listFieldUnitsByAssociatedTaxon(Set
<TaxonRelationshipEdge
> includeRelationships
,
306 Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
308 if(!getSession().contains(associatedTaxon
)){
309 associatedTaxon
= (Taxon
) taxonService
.load(associatedTaxon
.getUuid());
312 Set
<FieldUnit
> fieldUnits
= new HashSet
<FieldUnit
>();
314 List
<SpecimenOrObservationBase
> records
= pageByAssociatedTaxon(null, includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
).getRecords();
315 for(SpecimenOrObservationBase
<?
> specimen
:records
){
316 fieldUnits
.addAll(getFieldUnits(specimen
.getUuid()));
322 public DerivateHierarchyDTO
assembleDerivateHierarchyDTO(FieldUnit fieldUnit
, UUID associatedTaxonUuid
){
324 if(!getSession().contains(fieldUnit
)){
325 fieldUnit
= (FieldUnit
) load(fieldUnit
.getUuid());
327 TaxonBase associatedTaxon
= taxonService
.load(associatedTaxonUuid
);
329 DerivateHierarchyDTO dto
= new DerivateHierarchyDTO();
330 Map
<UUID
, TypeDesignationStatusBase
> typeSpecimenUUIDtoTypeDesignationStatus
= new HashMap
<UUID
, TypeDesignationStatusBase
>();
332 //gather types for this taxon name
333 TaxonNameBase
<?
,?
> name
= associatedTaxon
.getName();
334 Set
<?
> typeDesignations
= name
.getSpecimenTypeDesignations();
335 for (Object object
: typeDesignations
) {
336 if(object
instanceof SpecimenTypeDesignation
){
337 SpecimenTypeDesignation specimenTypeDesignation
= (SpecimenTypeDesignation
)object
;
338 DerivedUnit typeSpecimen
= specimenTypeDesignation
.getTypeSpecimen();
339 final TypeDesignationStatusBase typeStatus
= specimenTypeDesignation
.getTypeStatus();
340 typeSpecimenUUIDtoTypeDesignationStatus
.put(typeSpecimen
.getUuid(), typeStatus
);
344 if(fieldUnit
.getGatheringEvent()!=null){
345 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
347 final NamedArea country
= gatheringEvent
.getCountry();
348 dto
.setCountry(country
!=null?country
.getDescription():"");
350 final AgentBase collector
= gatheringEvent
.getCollector();
351 final String fieldNumber
= fieldUnit
.getFieldNumber();
352 dto
.setCollection(((collector
!=null?collector
:"") + " " + (fieldNumber
!=null?fieldNumber
:"")).trim());
354 final Partial gatheringDate
= gatheringEvent
.getGatheringDate();
355 dto
.setDate(gatheringDate
!=null?gatheringDate
.toString():"");
359 dto
.setTaxonName(associatedTaxon
.getName().getFullTitleCache());
362 Collection
<DerivedUnit
> derivedUnits
= new ArrayList
<DerivedUnit
>();
363 getDerivedUnitsFor(fieldUnit
, derivedUnits
);
366 Map
<eu
.etaxonomy
.cdm
.model
.occurrence
.Collection
, Integer
> collectionToCountMap
= new HashMap
<eu
.etaxonomy
.cdm
.model
.occurrence
.Collection
, Integer
>();
367 //List of accession numbers for citation
368 List
<String
> preservedSpecimenAccessionNumbers
= new ArrayList
<String
>();
370 //iterate over sub derivates
371 for (DerivedUnit derivedUnit
: derivedUnits
) {
372 //current accession number
373 String currentAccessionNumber
= derivedUnit
.getAccessionNumber()!=null?derivedUnit
.getAccessionNumber():"";
375 String currentHerbarium
= "";
376 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= derivedUnit
.getCollection();
377 if(collection
!=null){
378 currentHerbarium
= collection
.getCode()!=null?collection
.getCode():"";
380 Integer count
= collectionToCountMap
.get(collection
);
387 collectionToCountMap
.put(collection
, count
);
389 //check if derived unit is a type
390 if(typeSpecimenUUIDtoTypeDesignationStatus
.keySet().contains(derivedUnit
.getUuid())){
391 dto
.setHasType(true);
392 TypeDesignationStatusBase typeDesignationStatus
= typeSpecimenUUIDtoTypeDesignationStatus
.get(derivedUnit
.getUuid());
393 String typeStatus
= typeDesignationStatus
.getLabel();
394 dto
.addTypes(typeStatus
, currentAccessionNumber
);
396 //assemble molecular data
397 if(derivedUnit
instanceof DnaSample
){//.getRecordBasis()==SpecimenOrObservationType.DnaSample){
400 DnaSample dna
= (DnaSample
)derivedUnit
;
401 for(Sequence sequence
:dna
.getSequences()){
402 final URI boldUri
= sequence
.getBoldUri();
403 final DefinedTerm dnaMarker
= sequence
.getDnaMarker();
404 dto
.addMolecularData(boldUri
!=null?boldUri
.toString():"", dnaMarker
!=null?dnaMarker
.getLabel():"[no marker]");
407 //assemble media data
408 else if(derivedUnit
instanceof MediaSpecimen
){
410 MediaSpecimen media
= (MediaSpecimen
)derivedUnit
;
411 String mediaUriString
= getMediaUriString(media
);
412 if(media
.getKindOfUnit()!=null){
413 if(media
.getKindOfUnit().getUuid().equals(UUID
.fromString("acda15be-c0e2-4ea8-8783-b9b0c4ad7f03"))){
414 dto
.setHasSpecimenScan(true);
415 if(mediaUriString
!=null){
416 final String imageLinkText
= currentHerbarium
+" "+currentAccessionNumber
;
417 dto
.addSpecimenScan(mediaUriString
, !imageLinkText
.equals(" ")?imageLinkText
:"[no accession]");
420 else if(media
.getKindOfUnit().getUuid().equals(UUID
.fromString("31eb8d02-bf5d-437c-bcc6-87a626445f34"))){
421 dto
.setHasDetailImage(true);
422 if(mediaUriString
!=null){
424 if(media
.getMediaSpecimen()!=null && media
.getMediaSpecimen().getTitle()!=null){
425 motif
= media
.getMediaSpecimen().getTitle().getText();
427 dto
.addDetailImage(mediaUriString
, motif
!=null?motif
:"[no motif]");
432 //assemble preserved specimen data
433 else if(derivedUnit
.getRecordBasis()==SpecimenOrObservationType
.PreservedSpecimen
){
434 if(!currentAccessionNumber
.isEmpty()){
435 preservedSpecimenAccessionNumbers
.add(currentAccessionNumber
);
440 final String separator
= ", ";
442 String citation
= "";
443 citation
+= !dto
.getCountry().isEmpty()?dto
.getCountry()+separator
:"";
444 if(fieldUnit
.getGatheringEvent()!=null){
445 if(fieldUnit
.getGatheringEvent().getLocality()!=null){
446 citation
+= fieldUnit
.getGatheringEvent().getLocality().getText();
447 citation
+= separator
;
449 if(fieldUnit
.getGatheringEvent().getExactLocation()!=null
450 && fieldUnit
.getGatheringEvent().getExactLocation().getLatitude()!=null
451 && fieldUnit
.getGatheringEvent().getExactLocation().getLongitude()!=null){
452 citation
+= fieldUnit
.getGatheringEvent().getExactLocation().getLatitude().toString();
453 citation
+= separator
;
454 citation
+= fieldUnit
.getGatheringEvent().getExactLocation().getLongitude().toString();
455 citation
+= separator
;
458 citation
+= !dto
.getCollection().isEmpty()?dto
.getCollection()+separator
:"";
459 if(!preservedSpecimenAccessionNumbers
.isEmpty()){
461 for(String accessionNumber
:preservedSpecimenAccessionNumbers
){
462 if(!accessionNumber
.isEmpty()){
463 citation
+= accessionNumber
+separator
;
466 citation
= removeTail(citation
, separator
);
469 citation
= removeTail(citation
, separator
);
470 dto
.setCitation(citation
);
472 //assemble herbaria string
473 String herbariaString
= "";
474 for(Entry
<eu
.etaxonomy
.cdm
.model
.occurrence
.Collection
, Integer
> e
:collectionToCountMap
.entrySet()){
475 eu
.etaxonomy
.cdm
.model
.occurrence
.Collection collection
= e
.getKey();
476 if(collection
.getCode()!=null){
477 herbariaString
+= collection
.getCode();
480 herbariaString
+= "("+e
.getValue()+")";
482 herbariaString
+= separator
;
484 herbariaString
= removeTail(herbariaString
, separator
);
485 dto
.setHerbarium(herbariaString
);
496 private String
removeTail(String string
, final String tail
) {
497 if(string
.endsWith(tail
)){
498 string
= string
.substring(0, string
.length()-tail
.length());
503 private String
getMediaUriString(MediaSpecimen mediaSpecimen
){
504 String mediaUri
= null;
505 Collection
<MediaRepresentation
> mediaRepresentations
= mediaSpecimen
.getMediaSpecimen().getRepresentations();
506 if(mediaRepresentations
!=null && !mediaRepresentations
.isEmpty()){
507 Collection
<MediaRepresentationPart
> mediaRepresentationParts
= mediaRepresentations
.iterator().next().getParts();
508 if(mediaRepresentationParts
!=null && !mediaRepresentationParts
.isEmpty()){
509 MediaRepresentationPart part
= mediaRepresentationParts
.iterator().next();
510 if(part
.getUri()!=null){
511 mediaUri
= part
.getUri().toASCIIString();
518 private void getDerivedUnitsFor(SpecimenOrObservationBase
<?
> specimen
, Collection
<DerivedUnit
> derivedUnits
){
519 for(DerivationEvent derivationEvent
:specimen
.getDerivationEvents()){
520 for(DerivedUnit derivative
:derivationEvent
.getDerivatives()){
521 derivedUnits
.add(derivative
);
522 getDerivedUnitsFor(derivative
, derivedUnits
);
529 * @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)
531 @SuppressWarnings("unchecked")
533 public <T
extends SpecimenOrObservationBase
> Pager
<T
> pageByAssociatedTaxon(Class
<T
> type
, Set
<TaxonRelationshipEdge
> includeRelationships
,
534 Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
536 Set
<Taxon
> taxa
= new HashSet
<Taxon
>();
537 Set
<Integer
> occurrenceIds
= new HashSet
<Integer
>();
538 List
<T
> occurrences
= new ArrayList
<T
>();
540 // Integer limit = PagerUtils.limitFor(pageSize);
541 // Integer start = PagerUtils.startFor(pageSize, pageNumber);
543 if(!getSession().contains(associatedTaxon
)){
544 associatedTaxon
= (Taxon
) taxonService
.load(associatedTaxon
.getUuid());
547 if(includeRelationships
!= null) {
548 taxa
= taxonService
.listRelatedTaxa(associatedTaxon
, includeRelationships
, maxDepth
, null, null, propertyPaths
);
551 taxa
.add(associatedTaxon
);
553 for (Taxon taxon
: taxa
) {
554 List
<T
> perTaxonOccurrences
= dao
.listByAssociatedTaxon(type
, taxon
, null, null, orderHints
, propertyPaths
);
555 for (SpecimenOrObservationBase o
: perTaxonOccurrences
) {
556 occurrenceIds
.add(o
.getId());
559 occurrences
= (List
<T
>) dao
.listByIds(occurrenceIds
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
561 return new DefaultPagerImpl
<T
>(pageNumber
, occurrenceIds
.size(), pageSize
, occurrences
);
566 * @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)
568 @SuppressWarnings("unchecked")
570 public <T
extends SpecimenOrObservationBase
> Pager
<T
> pageByAssociatedTaxon(Class
<T
> type
, Set
<TaxonRelationshipEdge
> includeRelationships
,
571 String taxonUUID
, Integer maxDepth
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
573 UUID uuid
= UUID
.fromString(taxonUUID
);
574 Taxon tax
= (Taxon
) taxonService
.load(uuid
);
575 //TODO REMOVE NULL STATEMENT
577 return pageByAssociatedTaxon( type
,includeRelationships
,tax
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
583 public Pager
<SearchResult
<SpecimenOrObservationBase
>> findByFullText(
584 Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, Rectangle boundingBox
, List
<Language
> languages
,
585 boolean highlightFragments
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
,
586 List
<String
> propertyPaths
) throws CorruptIndexException
, IOException
, ParseException
{
588 LuceneSearch luceneSearch
= prepareByFullTextSearch(clazz
, queryString
, boundingBox
, languages
, highlightFragments
);
590 // --- execute search
591 TopGroupsWithMaxScore topDocsResultSet
= luceneSearch
.executeSearch(pageSize
, pageNumber
);
593 Map
<CdmBaseType
, String
> idFieldMap
= new HashMap
<CdmBaseType
, String
>();
594 idFieldMap
.put(CdmBaseType
.SPECIMEN_OR_OBSERVATIONBASE
, "id");
596 // --- initialize taxa, highlight matches ....
597 ISearchResultBuilder searchResultBuilder
= new SearchResultBuilder(luceneSearch
, luceneSearch
.getQuery());
598 @SuppressWarnings("rawtypes")
599 List
<SearchResult
<SpecimenOrObservationBase
>> searchResults
= searchResultBuilder
.createResultSet(
600 topDocsResultSet
, luceneSearch
.getHighlightFields(), dao
, idFieldMap
, propertyPaths
);
602 int totalHits
= topDocsResultSet
!= null ? topDocsResultSet
.topGroups
.totalGroupCount
: 0;
604 return new DefaultPagerImpl
<SearchResult
<SpecimenOrObservationBase
>>(pageNumber
, totalHits
, pageSize
,
614 * @param highlightFragments
617 private LuceneSearch
prepareByFullTextSearch(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, Rectangle bbox
,
618 List
<Language
> languages
, boolean highlightFragments
) {
620 BooleanQuery finalQuery
= new BooleanQuery();
621 BooleanQuery textQuery
= new BooleanQuery();
623 LuceneSearch luceneSearch
= new LuceneSearch(luceneIndexToolProvider
, FieldUnit
.class);
624 QueryFactory queryFactory
= luceneIndexToolProvider
.newQueryFactoryFor(FieldUnit
.class);
627 luceneSearch
.setCdmTypRestriction(clazz
);
628 if(queryString
!= null){
629 textQuery
.add(queryFactory
.newTermQuery("titleCache", queryString
), Occur
.SHOULD
);
630 finalQuery
.add(textQuery
, Occur
.MUST
);
635 finalQuery
.add(QueryFactory
.buildSpatialQueryByRange(bbox
, "gatheringEvent.exactLocation.point"), Occur
.MUST
);
638 luceneSearch
.setQuery(finalQuery
);
641 SortField
[] sortFields
= new SortField
[]{SortField
.FIELD_SCORE
, new SortField("titleCache__sort", SortField
.STRING
, false)};
642 luceneSearch
.setSortFields(sortFields
);
644 if(highlightFragments
){
645 luceneSearch
.setHighlightFields(queryFactory
.getTextFieldNamesAsArray());
652 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(eu.etaxonomy.cdm.model.occurrence.DerivedUnit)
655 public Collection
<FieldUnit
> getFieldUnits(UUID derivedUnitUuid
) {
656 //It will search recursively over all {@link DerivationEvent}s and get the "originals" ({@link SpecimenOrObservationBase})
657 //from which this DerivedUnit was derived until all FieldUnits are found.
659 //FIXME: use HQL queries to increase performance
660 SpecimenOrObservationBase
<?
> specimen
= load(derivedUnitUuid
);
661 // specimen = HibernateProxyHelper.deproxy(specimen, SpecimenOrObservationBase.class);
662 Collection
<FieldUnit
> fieldUnits
= new ArrayList
<FieldUnit
>();
664 if(specimen
instanceof FieldUnit
){
665 fieldUnits
.add((FieldUnit
) specimen
);
667 else if(specimen
instanceof DerivedUnit
){
668 getFieldUnits((DerivedUnit
) specimen
, fieldUnits
);
678 private void getFieldUnits(DerivedUnit derivedUnit
, Collection
<FieldUnit
> fieldUnits
) {
679 Set
<SpecimenOrObservationBase
> originals
= derivedUnit
.getOriginals();
680 if(originals
!=null && !originals
.isEmpty()){
681 for(SpecimenOrObservationBase
<?
> original
:originals
){
682 if(original
instanceof FieldUnit
){
683 fieldUnits
.add((FieldUnit
) original
);
685 else if(original
instanceof DerivedUnit
){
686 getFieldUnits((DerivedUnit
) original
, fieldUnits
);
693 * @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)
696 public boolean moveSequence(DnaSample from
, DnaSample to
, Sequence sequence
) {
697 //reload specimens to avoid session conflicts
698 from
= (DnaSample
) load(from
.getUuid());
699 to
= (DnaSample
) load(to
.getUuid());
700 sequence
= sequenceService
.load(sequence
.getUuid());
702 if(from
==null || to
==null || sequence
==null){
703 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" +
704 "Operation was move "+sequence
+ " from "+from
+" to "+to
);
706 from
.removeSequence(sequence
);
708 to
.addSequence(sequence
);
714 * @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)
717 public boolean moveDerivate(SpecimenOrObservationBase
<?
> from
, SpecimenOrObservationBase
<?
> to
, DerivedUnit derivate
) {
718 //reload specimens to avoid session conflicts
719 from
= load(from
.getUuid());
720 to
= load(to
.getUuid());
721 derivate
= (DerivedUnit
) load(derivate
.getUuid());
723 if(from
==null || to
==null || derivate
==null){
724 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" +
725 "Operation was move "+derivate
+ " from "+from
+" to "+to
);
728 SpecimenOrObservationType derivateType
= derivate
.getRecordBasis();
729 SpecimenOrObservationType toType
= to
.getRecordBasis();
730 //check if type is a sub derivate type
731 if(toType
==SpecimenOrObservationType
.FieldUnit
//moving to FieldUnit always works
732 || derivateType
==SpecimenOrObservationType
.Media
//moving media always works
733 || (derivateType
.isKindOf(toType
) && toType
!=derivateType
)){ //moving only to parent derivate type
734 //remove derivation event from parent specimen of dragged object
735 DerivationEvent eventToRemove
= null;
736 for(DerivationEvent event
:from
.getDerivationEvents()){
737 if(event
.getDerivatives().contains(derivate
)){
738 eventToRemove
= event
;
742 from
.removeDerivationEvent(eventToRemove
);
744 //add new derivation event to target
745 to
.addDerivationEvent(DerivationEvent
.NewSimpleInstance(to
, derivate
, eventToRemove
==null?
null:eventToRemove
.getType()));
753 public Collection
<ICdmBase
> getNonCascadedAssociatedElements(SpecimenOrObservationBase
<?
> specimen
){
754 //potential fields that are not persisted cascadingly
767 --CollectingAreas TERM
775 -storedUnder CDM TaxonNameBase
778 Collection
<ICdmBase
> nonCascadedCdmEntities
= new HashSet
<ICdmBase
>();
779 //scan SpecimenOrObservationBase
780 for(DeterminationEvent determinationEvent
:specimen
.getDeterminations()){
782 if(determinationEvent
.getModifier()!=null){
783 nonCascadedCdmEntities
.add(determinationEvent
.getModifier());
787 if(specimen
.getKindOfUnit()!=null){
788 nonCascadedCdmEntities
.add(specimen
.getKindOfUnit());
791 if(specimen
.getLifeStage()!=null){
792 nonCascadedCdmEntities
.add(specimen
.getLifeStage());
795 if(specimen
.getSex()!=null){
796 nonCascadedCdmEntities
.add(specimen
.getSex());
800 if(specimen
instanceof FieldUnit
){
801 nonCascadedCdmEntities
.addAll(getNonCascadedAssociatedElements((FieldUnit
)specimen
));
804 else if(specimen
instanceof DerivedUnit
){
805 DerivedUnit derivedUnit
= (DerivedUnit
)specimen
;
806 if(derivedUnit
.getDerivedFrom()!=null){
807 Collection
<FieldUnit
> fieldUnits
= new ArrayList
<FieldUnit
>();
808 getFieldUnits(derivedUnit
, fieldUnits
);
809 for(FieldUnit fieldUnit
:fieldUnits
){
810 nonCascadedCdmEntities
.addAll(getNonCascadedAssociatedElements(fieldUnit
));
814 return nonCascadedCdmEntities
;
817 private Collection
<ICdmBase
> getNonCascadedAssociatedElements(FieldUnit fieldUnit
){
818 Collection
<ICdmBase
> nonCascadedCdmEntities
= new HashSet
<ICdmBase
>();
819 GatheringEvent gatheringEvent
= fieldUnit
.getGatheringEvent();
820 if(gatheringEvent
!=null){
822 if(gatheringEvent
.getCountry()!=null){
823 nonCascadedCdmEntities
.add(gatheringEvent
.getCountry());
826 for (NamedArea namedArea
: gatheringEvent
.getCollectingAreas()) {
827 nonCascadedCdmEntities
.add(namedArea
);
830 for (DerivationEvent derivationEvent
: fieldUnit
.getDerivationEvents()) {
831 for (DerivedUnit derivedUnit
: derivationEvent
.getDerivatives()) {
832 nonCascadedCdmEntities
.addAll(getNonCascadedAssociatedElements(derivedUnit
));
835 return nonCascadedCdmEntities
;
838 private Collection
<ICdmBase
> getNonCascadedAssociatedElements(DerivedUnit derivedUnit
){
839 Collection
<ICdmBase
> nonCascadedCdmEntities
= new HashSet
<ICdmBase
>();
840 if(derivedUnit
.getCollection()!=null && derivedUnit
.getCollection().getInstitute()!=null){
841 for (DefinedTerm type
: derivedUnit
.getCollection().getInstitute().getTypes()) {
842 nonCascadedCdmEntities
.add(type
);
845 if(derivedUnit
.getPreservation()!=null && derivedUnit
.getPreservation().getMedium()!=null){
846 nonCascadedCdmEntities
.add(derivedUnit
.getPreservation().getMedium());
848 if(derivedUnit
.getStoredUnder()!=null){
849 nonCascadedCdmEntities
.add(derivedUnit
.getStoredUnder());
851 return nonCascadedCdmEntities
;