3 * Copyright (C) 2013 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.
10 package eu
.etaxonomy
.taxeditor
.editor
.view
.dataimport
.transientServices
;
12 import java
.io
.IOException
;
13 import java
.util
.Collection
;
14 import java
.util
.HashSet
;
15 import java
.util
.List
;
18 import java
.util
.UUID
;
20 import org
.apache
.lucene
.index
.CorruptIndexException
;
21 import org
.apache
.lucene
.queryParser
.ParseException
;
22 import org
.hibernate
.LockOptions
;
23 import org
.hibernate
.Session
;
24 import org
.hibernate
.criterion
.Criterion
;
25 import org
.hibernate
.envers
.query
.criteria
.AuditCriterion
;
26 import org
.hibernate
.search
.spatial
.impl
.Rectangle
;
28 import eu
.etaxonomy
.cdm
.api
.facade
.DerivedUnitFacade
;
29 import eu
.etaxonomy
.cdm
.api
.facade
.DerivedUnitFacadeNotSupportedException
;
30 import eu
.etaxonomy
.cdm
.api
.service
.DeleteResult
;
31 import eu
.etaxonomy
.cdm
.api
.service
.IOccurrenceService
;
32 import eu
.etaxonomy
.cdm
.api
.service
.UpdateResult
;
33 import eu
.etaxonomy
.cdm
.api
.service
.config
.DeleteConfiguratorBase
;
34 import eu
.etaxonomy
.cdm
.api
.service
.config
.IIdentifiableEntityServiceConfigurator
;
35 import eu
.etaxonomy
.cdm
.api
.service
.config
.SpecimenDeleteConfigurator
;
36 import eu
.etaxonomy
.cdm
.api
.service
.dto
.FieldUnitDTO
;
37 import eu
.etaxonomy
.cdm
.api
.service
.dto
.FindByIdentifierDTO
;
38 import eu
.etaxonomy
.cdm
.api
.service
.dto
.PreservedSpecimenDTO
;
39 import eu
.etaxonomy
.cdm
.api
.service
.pager
.Pager
;
40 import eu
.etaxonomy
.cdm
.api
.service
.search
.SearchResult
;
41 import eu
.etaxonomy
.cdm
.api
.service
.util
.TaxonRelationshipEdge
;
42 import eu
.etaxonomy
.cdm
.common
.monitor
.IProgressMonitor
;
43 import eu
.etaxonomy
.cdm
.model
.common
.Annotation
;
44 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
45 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTerm
;
46 import eu
.etaxonomy
.cdm
.model
.common
.ICdmBase
;
47 import eu
.etaxonomy
.cdm
.model
.common
.ISourceable
;
48 import eu
.etaxonomy
.cdm
.model
.common
.IdentifiableSource
;
49 import eu
.etaxonomy
.cdm
.model
.common
.LSID
;
50 import eu
.etaxonomy
.cdm
.model
.common
.Language
;
51 import eu
.etaxonomy
.cdm
.model
.common
.Marker
;
52 import eu
.etaxonomy
.cdm
.model
.common
.MarkerType
;
53 import eu
.etaxonomy
.cdm
.model
.description
.DescriptionBase
;
54 import eu
.etaxonomy
.cdm
.model
.description
.DescriptionElementBase
;
55 import eu
.etaxonomy
.cdm
.model
.description
.IndividualsAssociation
;
56 import eu
.etaxonomy
.cdm
.model
.location
.Country
;
57 import eu
.etaxonomy
.cdm
.model
.media
.Media
;
58 import eu
.etaxonomy
.cdm
.model
.media
.Rights
;
59 import eu
.etaxonomy
.cdm
.model
.molecular
.DnaSample
;
60 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
61 import eu
.etaxonomy
.cdm
.model
.molecular
.SingleRead
;
62 import eu
.etaxonomy
.cdm
.model
.name
.SpecimenTypeDesignation
;
63 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivationEvent
;
64 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivedUnit
;
65 import eu
.etaxonomy
.cdm
.model
.occurrence
.DeterminationEvent
;
66 import eu
.etaxonomy
.cdm
.model
.occurrence
.FieldUnit
;
67 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationBase
;
68 import eu
.etaxonomy
.cdm
.model
.taxon
.Taxon
;
69 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonBase
;
70 import eu
.etaxonomy
.cdm
.model
.view
.AuditEvent
;
71 import eu
.etaxonomy
.cdm
.model
.view
.AuditEventRecord
;
72 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.AuditEventSort
;
73 import eu
.etaxonomy
.cdm
.persistence
.dto
.MergeResult
;
74 import eu
.etaxonomy
.cdm
.persistence
.dto
.UuidAndTitleCache
;
75 import eu
.etaxonomy
.cdm
.persistence
.query
.Grouping
;
76 import eu
.etaxonomy
.cdm
.persistence
.query
.MatchMode
;
77 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
;
78 import eu
.etaxonomy
.cdm
.strategy
.cache
.common
.IIdentifiableEntityCacheStrategy
;
79 import eu
.etaxonomy
.cdm
.strategy
.match
.IMatchStrategy
;
80 import eu
.etaxonomy
.cdm
.strategy
.merge
.IMergeStrategy
;
87 public class TransientOccurenceService
implements IOccurrenceService
{
89 private final IOccurrenceService defaultService
;
90 private final Collection
<SpecimenOrObservationBase
<?
>> units
;
93 * @param defaultService
95 public TransientOccurenceService(IOccurrenceService defaultService
) {
96 this.defaultService
= defaultService
;
97 this.units
= new HashSet
<SpecimenOrObservationBase
<?
>>();
105 * @param propertyPaths
107 * @see eu.etaxonomy.cdm.api.service.IVersionableService#pageAuditEvents(eu.etaxonomy.cdm.model.common.VersionableEntity, java.lang.Integer, java.lang.Integer, eu.etaxonomy.cdm.persistence.dao.common.AuditEventSort, java.util.List)
110 public Pager
<AuditEventRecord
<SpecimenOrObservationBase
>> pageAuditEvents(SpecimenOrObservationBase t
, Integer pageSize
, Integer pageNumber
, AuditEventSort sort
, List
<String
> propertyPaths
) {
111 return defaultService
.pageAuditEvents(t
, pageSize
, pageNumber
, sort
, propertyPaths
);
115 * @param annotatedObj
120 * @param propertyPaths
122 * @see eu.etaxonomy.cdm.api.service.IAnnotatableService#getAnnotations(eu.etaxonomy.cdm.model.common.AnnotatableEntity, eu.etaxonomy.cdm.model.common.MarkerType, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
125 public Pager
<Annotation
> getAnnotations(SpecimenOrObservationBase annotatedObj
, MarkerType status
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
126 return defaultService
.getAnnotations(annotatedObj
, status
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
131 * @see eu.etaxonomy.cdm.api.service.IService#clear()
134 public void clear() {
135 defaultService
.clear();
141 * @see eu.etaxonomy.cdm.api.service.IService#lock(eu.etaxonomy.cdm.model.common.ICdmBase, org.hibernate.LockMode)
144 public void lock(SpecimenOrObservationBase t
, LockOptions lockOptions
) {
145 defaultService
.lock(t
, lockOptions
);
151 * @param propertyPaths
152 * @see eu.etaxonomy.cdm.api.service.IService#refresh(eu.etaxonomy.cdm.model.common.ICdmBase, org.hibernate.LockMode, java.util.List)
155 public void refresh(SpecimenOrObservationBase t
, LockOptions lockOptions
, List
<String
> propertyPaths
) {
156 defaultService
.refresh(t
, lockOptions
, propertyPaths
);
161 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache()
164 public void updateTitleCache() {
165 defaultService
.updateTitleCache();
171 * @see eu.etaxonomy.cdm.api.service.IVersionableService#getNextAuditEvent(eu.etaxonomy.cdm.model.common.VersionableEntity)
174 public AuditEventRecord
<SpecimenOrObservationBase
> getNextAuditEvent(SpecimenOrObservationBase t
) {
175 return defaultService
.getNextAuditEvent(t
);
179 * @param annotatableEntity
184 * @param propertyPaths
186 * @see eu.etaxonomy.cdm.api.service.IAnnotatableService#getMarkers(eu.etaxonomy.cdm.model.common.AnnotatableEntity, java.lang.Boolean, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
189 public Pager
<Marker
> getMarkers(SpecimenOrObservationBase annotatableEntity
, Boolean technical
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
190 return defaultService
.getMarkers(annotatableEntity
, technical
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
196 * @param cacheStrategy
198 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache(java.lang.Class, java.lang.Integer, eu.etaxonomy.cdm.strategy.cache.common.IIdentifiableEntityCacheStrategy, eu.etaxonomy.cdm.common.monitor.IProgressMonitor)
201 public void updateTitleCache(Class
<?
extends SpecimenOrObservationBase
> clazz
, Integer stepSize
, IIdentifiableEntityCacheStrategy
<SpecimenOrObservationBase
> cacheStrategy
, IProgressMonitor monitor
) {
202 defaultService
.updateTitleCache(clazz
, stepSize
, cacheStrategy
, monitor
);
208 * @see eu.etaxonomy.cdm.api.service.IVersionableService#getPreviousAuditEvent(eu.etaxonomy.cdm.model.common.VersionableEntity)
211 public AuditEventRecord
<SpecimenOrObservationBase
> getPreviousAuditEvent(SpecimenOrObservationBase t
) {
212 return defaultService
.getPreviousAuditEvent(t
);
218 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getCountryByIso(java.lang.String)
221 public Country
getCountryByIso(String iso639
) {
222 return defaultService
.getCountryByIso(iso639
);
228 * @see eu.etaxonomy.cdm.api.service.IService#count(java.lang.Class)
231 public int count(Class
<?
extends SpecimenOrObservationBase
> clazz
) {
232 return defaultService
.count(clazz
);
238 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getCountryByName(java.lang.String)
241 public List
<Country
> getCountryByName(String name
) {
242 return defaultService
.getCountryByName(name
);
247 * @param determinedAs
251 * @param propertyPaths
253 * @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)
256 public Pager
<SpecimenOrObservationBase
> list(Class
<?
extends SpecimenOrObservationBase
> type
, TaxonBase determinedAs
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
257 return defaultService
.list(type
, determinedAs
, limit
, start
, orderHints
, propertyPaths
);
268 * @param propertyPaths
270 * @see eu.etaxonomy.cdm.api.service.IVersionableService#pageAuditEvents(java.lang.Class, eu.etaxonomy.cdm.model.view.AuditEvent, eu.etaxonomy.cdm.model.view.AuditEvent, java.util.List, java.lang.Integer, java.lang.Integer, eu.etaxonomy.cdm.persistence.dao.common.AuditEventSort, java.util.List)
273 public Pager
<AuditEventRecord
<SpecimenOrObservationBase
>> pageAuditEvents(Class
<?
extends SpecimenOrObservationBase
> clazz
, AuditEvent from
, AuditEvent to
, List
<AuditCriterion
> criteria
, Integer pageSize
, Integer pageValue
, AuditEventSort sort
, List
<String
> propertyPaths
) {
274 return defaultService
.pageAuditEvents(clazz
, from
, to
, criteria
, pageSize
, pageValue
, sort
, propertyPaths
);
280 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#find(eu.etaxonomy.cdm.model.common.LSID)
283 public SpecimenOrObservationBase
find(LSID lsid
) {
284 return defaultService
.find(lsid
);
288 * @param persistentObject
290 * @see eu.etaxonomy.cdm.api.service.IService#delete(eu.etaxonomy.cdm.model.common.ICdmBase)
293 public DeleteResult
delete(SpecimenOrObservationBase persistentObject
) {
294 return defaultService
.delete(persistentObject
);
302 * @param propertyPaths
304 * @see eu.etaxonomy.cdm.api.service.IAnnotatableService#groupMarkers(java.lang.Class, java.lang.Boolean, java.lang.Integer, java.lang.Integer, java.util.List)
307 public List
<Object
[]> groupMarkers(Class
<?
extends SpecimenOrObservationBase
> clazz
, Boolean technical
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
308 return defaultService
.groupMarkers(clazz
, technical
, pageSize
, pageNumber
, propertyPaths
);
314 * @see eu.etaxonomy.cdm.api.service.IService#exists(java.util.UUID)
317 public boolean exists(UUID uuid
) {
318 return defaultService
.exists(uuid
);
325 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#replace(eu.etaxonomy.cdm.model.common.IdentifiableEntity, eu.etaxonomy.cdm.model.common.IdentifiableEntity)
328 public SpecimenOrObservationBase
replace(SpecimenOrObservationBase x
, SpecimenOrObservationBase y
) {
329 return defaultService
.replace(x
, y
);
335 * @see eu.etaxonomy.cdm.api.service.IService#find(java.util.Set)
338 public List
<SpecimenOrObservationBase
> find(Set
<UUID
> uuidSet
) {
339 return defaultService
.find(uuidSet
);
346 * @param propertyPaths
348 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getSources(eu.etaxonomy.cdm.model.common.IdentifiableEntity, java.lang.Integer, java.lang.Integer, java.util.List)
351 public Pager
<IdentifiableSource
> getSources(SpecimenOrObservationBase t
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
352 return defaultService
.getSources(t
, pageSize
, pageNumber
, propertyPaths
);
358 * @see eu.etaxonomy.cdm.api.service.IService#find(java.util.UUID)
361 public SpecimenOrObservationBase
find(UUID uuid
) {
362 return defaultService
.find(uuid
);
368 * @see eu.etaxonomy.cdm.api.service.IService#find(int)
371 public SpecimenOrObservationBase
find(int id
) {
372 return defaultService
.find(id
);
379 * @param propertyPaths
381 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getRights(eu.etaxonomy.cdm.model.common.IdentifiableEntity, java.lang.Integer, java.lang.Integer, java.util.List)
384 public Pager
<Rights
> getRights(SpecimenOrObservationBase t
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
385 return defaultService
.getRights(t
, pageSize
, pageNumber
, propertyPaths
);
392 * @see eu.etaxonomy.cdm.api.service.IAnnotatableService#countMarkers(java.lang.Class, java.lang.Boolean)
395 public int countMarkers(Class
<?
extends SpecimenOrObservationBase
> clazz
, Boolean technical
) {
396 return defaultService
.countMarkers(clazz
, technical
);
403 * @param propertyPaths
405 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getMedia(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List)
408 public Pager
<Media
> getMedia(SpecimenOrObservationBase occurence
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
409 return defaultService
.getMedia(occurence
, pageSize
, pageNumber
, propertyPaths
);
415 * @see eu.etaxonomy.cdm.api.service.IService#findById(java.util.Set)
418 public List
<SpecimenOrObservationBase
> findById(Set
<Integer
> idSet
) {
419 return defaultService
.findById(idSet
);
427 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getSourcedObjectByIdInSource(java.lang.Class, java.lang.String, java.lang.String)
430 public ISourceable
getSourcedObjectByIdInSource(Class clazz
, String idInSource
, String idNamespace
) {
431 return defaultService
.getSourcedObjectByIdInSource(clazz
, idInSource
, idNamespace
);
436 * @see eu.etaxonomy.cdm.api.service.IService#getSession()
439 public Session
getSession() {
440 return defaultService
.getSession();
445 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getUuidAndTitleCache()
448 public List
<UuidAndTitleCache
<SpecimenOrObservationBase
>> getUuidAndTitleCache() {
449 return defaultService
.getUuidAndTitleCache();
457 * @param propertyPaths
459 * @see eu.etaxonomy.cdm.api.service.IService#group(java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
462 public List
<Object
[]> group(Class
<?
extends SpecimenOrObservationBase
> clazz
, Integer limit
, Integer start
, List
<Grouping
> groups
, List
<String
> propertyPaths
) {
463 return defaultService
.group(clazz
, limit
, start
, groups
, propertyPaths
);
471 * @param propertyPaths
473 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase, java.lang.Integer, java.lang.Integer, java.util.List)
476 public Pager
<DeterminationEvent
> getDeterminations(SpecimenOrObservationBase occurence
, TaxonBase taxonBase
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
477 return defaultService
.getDeterminations(occurence
, taxonBase
, pageSize
, pageNumber
, propertyPaths
);
488 * @param propertyPaths
490 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#findByTitle(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.List, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
493 public Pager
<SpecimenOrObservationBase
> findByTitle(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, MatchMode matchmode
, List
<Criterion
> criteria
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
494 return defaultService
.findByTitle(clazz
, queryString
, matchmode
, criteria
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
501 * @param propertyPaths
503 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivationEvents(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List)
506 public Pager
<DerivationEvent
> getDerivationEvents(SpecimenOrObservationBase occurence
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
507 return defaultService
.getDerivationEvents(occurence
, pageSize
, pageNumber
, propertyPaths
);
515 * @param propertyPaths
517 * @see eu.etaxonomy.cdm.api.service.IService#list(java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
520 public <S
extends SpecimenOrObservationBase
> List
<S
> list(Class
<S
> type
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
521 return defaultService
.list(type
, limit
, start
, orderHints
, propertyPaths
);
530 * @param propertyPaths
532 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#search(java.lang.Class, java.lang.String, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
535 public Pager
<SpecimenOrObservationBase
> search(Class
<?
extends SpecimenOrObservationBase
> clazz
, String query
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
536 return defaultService
.search(clazz
, query
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
540 * @param configurator
542 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#findByTitle(eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator)
545 public Pager
<SpecimenOrObservationBase
> findByTitle(IIdentifiableEntityServiceConfigurator
<SpecimenOrObservationBase
> configurator
) {
546 return defaultService
.findByTitle(configurator
);
555 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#countByTitle(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.List)
558 public Integer
countByTitle(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, MatchMode matchmode
, List
<Criterion
> criteria
) {
559 return defaultService
.countByTitle(clazz
, queryString
, matchmode
, criteria
);
565 * @see eu.etaxonomy.cdm.api.service.IService#load(java.util.UUID)
568 public SpecimenOrObservationBase
load(UUID uuid
) {
569 return defaultService
.load(uuid
);
574 * @param propertyPaths
576 * @see eu.etaxonomy.cdm.api.service.IService#load(java.util.UUID, java.util.List)
579 public SpecimenOrObservationBase
load(UUID uuid
, List
<String
> propertyPaths
) {
580 return defaultService
.load(uuid
, propertyPaths
);
584 * @param configurator
586 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#countByTitle(eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator)
589 public Integer
countByTitle(IIdentifiableEntityServiceConfigurator
<SpecimenOrObservationBase
> configurator
) {
590 return defaultService
.countByTitle(configurator
);
595 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnitUuidAndTitleCache()
598 public List
<UuidAndTitleCache
<FieldUnit
>> getFieldUnitUuidAndTitleCache() {
599 return defaultService
.getFieldUnitUuidAndTitleCache();
604 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitUuidAndTitleCache()
607 public List
<UuidAndTitleCache
<DerivedUnit
>> getDerivedUnitUuidAndTitleCache() {
608 return defaultService
.getDerivedUnitUuidAndTitleCache();
612 * @param transientObject
614 * @see eu.etaxonomy.cdm.api.service.IService#merge(eu.etaxonomy.cdm.model.common.ICdmBase)
617 public SpecimenOrObservationBase
merge(SpecimenOrObservationBase transientObject
) {
618 return defaultService
.merge(transientObject
);
623 * @param propertyPaths
625 * @throws DerivedUnitFacadeNotSupportedException
626 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit, java.util.List)
629 public DerivedUnitFacade
getDerivedUnitFacade(DerivedUnit derivedUnit
, List
<String
> propertyPaths
) throws DerivedUnitFacadeNotSupportedException
{
630 return defaultService
.getDerivedUnitFacade(derivedUnit
, propertyPaths
);
641 * @param propertyPaths
643 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#listByTitle(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.List, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
646 public List
<SpecimenOrObservationBase
> listByTitle(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, MatchMode matchmode
, List
<Criterion
> criteria
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
647 return defaultService
.listByTitle(clazz
, queryString
, matchmode
, criteria
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
652 * @param propertyPaths
654 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
657 public List
<DerivedUnitFacade
> listDerivedUnitFacades(DescriptionBase description
, List
<String
> propertyPaths
) {
658 return defaultService
.listDerivedUnitFacades(description
, propertyPaths
);
666 * @param propertyPaths
668 * @see eu.etaxonomy.cdm.api.service.IService#page(java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
671 public <S
extends SpecimenOrObservationBase
> Pager
<S
> page(Class
<S
> type
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
672 return defaultService
.page(type
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
677 * @param includeRelationships
678 * @param associatedTaxon
683 * @param propertyPaths
685 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listByAssociatedTaxon(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)
688 public <T
extends SpecimenOrObservationBase
> List
<T
> listByAssociatedTaxon(Class
<T
> type
, Set
<TaxonRelationshipEdge
> includeRelationships
, Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
689 return defaultService
.listByAssociatedTaxon(type
, includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
693 * @param persistentObject
695 * @see eu.etaxonomy.cdm.api.service.IService#refresh(eu.etaxonomy.cdm.model.common.ICdmBase)
698 public UUID
refresh(SpecimenOrObservationBase persistentObject
) {
699 return defaultService
.refresh(persistentObject
);
710 * @param propertyPaths
712 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#listByReferenceTitle(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.List, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
715 public List
<SpecimenOrObservationBase
> listByReferenceTitle(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, MatchMode matchmode
, List
<Criterion
> criteria
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
716 return defaultService
.listByReferenceTitle(clazz
, queryString
, matchmode
, criteria
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
724 * @see eu.etaxonomy.cdm.api.service.IService#rows(java.lang.String, int, int)
727 public List
<SpecimenOrObservationBase
> rows(String tableName
, int limit
, int start
) {
728 return defaultService
.rows(tableName
, limit
, start
);
732 * @param newInstances
734 * @see eu.etaxonomy.cdm.api.service.IService#save(java.util.Collection)
737 public Map
<UUID
, SpecimenOrObservationBase
> save(Collection
<SpecimenOrObservationBase
> newInstances
) {
738 for(SpecimenOrObservationBase unit
:newInstances
){
746 * @param includeRelationships
747 * @param associatedTaxon
752 * @param propertyPaths
754 * @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)
757 public <T
extends SpecimenOrObservationBase
> Pager
<T
> pageByAssociatedTaxon(Class
<T
> type
, Set
<TaxonRelationshipEdge
> includeRelationships
, Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
758 return defaultService
.pageByAssociatedTaxon(type
, includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
764 * @see eu.etaxonomy.cdm.api.service.IService#save(eu.etaxonomy.cdm.model.common.ICdmBase)
767 public SpecimenOrObservationBase
save(SpecimenOrObservationBase newInstance
) {
768 units
.add(newInstance
);
773 * @param transientObject
775 * @see eu.etaxonomy.cdm.api.service.IService#saveOrUpdate(eu.etaxonomy.cdm.model.common.ICdmBase)
778 public UUID
saveOrUpdate(SpecimenOrObservationBase transientObject
) {
779 units
.add(transientObject
);
784 * @param transientObjects
786 * @see eu.etaxonomy.cdm.api.service.IService#saveOrUpdate(java.util.Collection)
789 public Map
<UUID
, SpecimenOrObservationBase
> saveOrUpdate(Collection
<SpecimenOrObservationBase
> transientObjects
) {
790 for(SpecimenOrObservationBase unit
:transientObjects
){
801 * @param highlightFragments
805 * @param propertyPaths
807 * @throws CorruptIndexException
808 * @throws IOException
809 * @throws ParseException
810 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#findByFullText(java.lang.Class, java.lang.String, org.hibernate.search.spatial.impl.Rectangle, java.util.List, boolean, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
813 public Pager
<SearchResult
<SpecimenOrObservationBase
>> findByFullText(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, Rectangle boundingBox
, List
<Language
> languages
, boolean highlightFragments
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) throws CorruptIndexException
, IOException
, ParseException
{
814 return defaultService
.findByFullText(clazz
, queryString
, boundingBox
, languages
, highlightFragments
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
818 * @param transientObject
820 * @see eu.etaxonomy.cdm.api.service.IService#update(eu.etaxonomy.cdm.model.common.ICdmBase)
823 public UUID
update(SpecimenOrObservationBase transientObject
) {
824 return defaultService
.update(transientObject
);
829 * @param includeProperties
833 * @param propertyPaths
835 * @see eu.etaxonomy.cdm.api.service.IService#list(eu.etaxonomy.cdm.model.common.ICdmBase, java.util.Set, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
838 public List
<SpecimenOrObservationBase
> list(SpecimenOrObservationBase example
, Set
<String
> includeProperties
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
839 return defaultService
.list(example
, includeProperties
, limit
, start
, orderHints
, propertyPaths
);
843 public int deduplicate(Class
<?
extends SpecimenOrObservationBase
> clazz
, IMatchStrategy matchStrategy
, IMergeStrategy mergeStrategy
) {
844 return defaultService
.deduplicate(clazz
, matchStrategy
, mergeStrategy
);
848 public Pager
<SpecimenOrObservationBase
> findTitleCache(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, MatchMode matchMode
) {
849 return defaultService
.findTitleCache(clazz
, queryString
, pageSize
, pageNumber
, orderHints
, matchMode
);
852 public Collection
<SpecimenOrObservationBase
<?
>> getUnits() {
857 public Collection
<FieldUnit
> getFieldUnits(UUID derivedUnitUuid
) {
858 return defaultService
.getFieldUnits(derivedUnitUuid
);
862 public <T
extends SpecimenOrObservationBase
> Pager
<T
> pageByAssociatedTaxon(Class
<T
> type
,
863 Set
<TaxonRelationshipEdge
> includeRelationships
, String taxonUUID
, Integer maxDepth
, Integer pageSize
,
864 Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
865 return defaultService
.pageByAssociatedTaxon(type
, includeRelationships
, taxonUUID
,
866 maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
871 public UpdateResult
moveSequence(DnaSample from
, DnaSample to
, Sequence sequence
) {
872 return defaultService
.moveSequence(from
, to
, sequence
);
876 public DeleteResult
isDeletable(SpecimenOrObservationBase object
,
877 DeleteConfiguratorBase config
) {
878 return defaultService
.isDeletable(object
, config
);
882 public int countDeterminations(SpecimenOrObservationBase occurence
, TaxonBase taxonbase
) {
883 return defaultService
.countDeterminations(occurence
, taxonbase
);
887 public SpecimenOrObservationBase
findWithoutFlush(UUID uuid
) {
888 return defaultService
.findWithoutFlush(uuid
);
892 public Collection
<SpecimenOrObservationBase
> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon
,
893 List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
894 return defaultService
.listFieldUnitsByAssociatedTaxon(associatedTaxon
, orderHints
, propertyPaths
);
898 public Pager
<SpecimenOrObservationBase
> pageFieldUnitsByAssociatedTaxon(
899 Set
<TaxonRelationshipEdge
> includeRelationships
, Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
,
900 Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
901 return defaultService
.pageFieldUnitsByAssociatedTaxon(includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
906 public FieldUnitDTO
assembleFieldUnitDTO(FieldUnit fieldUnit
, UUID associatedTaxonUuid
) {
907 return defaultService
.assembleFieldUnitDTO(fieldUnit
, associatedTaxonUuid
);
911 public PreservedSpecimenDTO
assemblePreservedSpecimenDTO(DerivedUnit derivedUnit
) {
912 return defaultService
.assemblePreservedSpecimenDTO(derivedUnit
);
916 public Collection
<ICdmBase
> getNonCascadedAssociatedElements(SpecimenOrObservationBase
<?
> specimen
) {
917 return defaultService
.getNonCascadedAssociatedElements(specimen
);
921 public DeleteResult
deleteDerivateHierarchy(CdmBase from
, SpecimenDeleteConfigurator config
) {
922 return defaultService
.deleteDerivateHierarchy(from
, config
);
926 public DeleteResult
delete(SpecimenOrObservationBase
<?
> specimen
, SpecimenDeleteConfigurator config
) {
927 return defaultService
.delete(specimen
, config
);
931 public Collection
<IndividualsAssociation
> listIndividualsAssociations(SpecimenOrObservationBase
<?
> specimen
,
932 Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
933 return defaultService
.listIndividualsAssociations(specimen
, limit
, start
, orderHints
, propertyPaths
);
937 public Collection
<SpecimenTypeDesignation
> listTypeDesignations(SpecimenOrObservationBase
<?
> specimen
,
938 Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
939 return defaultService
.listTypeDesignations(specimen
, limit
, start
, orderHints
, propertyPaths
);
943 public Collection
<DescriptionBase
<?
>> listDescriptionsWithDescriptionSpecimen(
944 SpecimenOrObservationBase
<?
> specimen
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
,
945 List
<String
> propertyPaths
) {
946 return defaultService
.listDescriptionsWithDescriptionSpecimen(specimen
, limit
, start
, orderHints
, propertyPaths
);
950 public <S
extends SpecimenOrObservationBase
> Pager
<FindByIdentifierDTO
<S
>> findByIdentifier(Class
<S
> clazz
, String identifier
, DefinedTerm identifierType
, MatchMode matchmode
, boolean includeEntity
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
){
951 return defaultService
.findByIdentifier(clazz
, identifier
, identifierType
, matchmode
, includeEntity
, pageSize
, pageNumber
, propertyPaths
);
955 public Collection
<DescriptionElementBase
> getCharacterDataForSpecimen(SpecimenOrObservationBase
<?
> arg0
) {
956 return defaultService
.getCharacterDataForSpecimen(arg0
);
960 public Collection
<DescriptionElementBase
> getCharacterDataForSpecimen(UUID arg0
) {
961 return getCharacterDataForSpecimen(arg0
);
965 public String
getMostSignificantIdentifier(DerivedUnit derivedUnit
) {
966 return defaultService
.getMostSignificantIdentifier(derivedUnit
);
970 public int countOccurrences(IIdentifiableEntityServiceConfigurator
<SpecimenOrObservationBase
> config
) {
971 return defaultService
.countOccurrences(config
);
978 public List
<DerivedUnit
> getAllChildDerivatives(SpecimenOrObservationBase
<?
> specimen
) {
979 return defaultService
.getAllChildDerivatives(specimen
);
986 public List
<SpecimenOrObservationBase
<?
>> getAllHierarchyDerivatives(SpecimenOrObservationBase
<?
> specimen
) {
987 return defaultService
.getAllHierarchyDerivatives(specimen
);
992 * @see eu.etaxonomy.cdm.api.service.IService#delete(java.util.UUID)
995 public DeleteResult
delete(UUID uuid
) {
996 return defaultService
.delete(uuid
);
1000 public DeleteResult
delete(Collection
<UUID
> arg0
) {
1001 return defaultService
.delete(arg0
);
1005 public DeleteResult
deleteSingleRead(SingleRead singleRead
, Sequence sequence
){
1006 return defaultService
.deleteSingleRead(singleRead
, sequence
);
1010 * @see eu.etaxonomy.cdm.api.service.IService#merge(java.util.List)
1013 public List
<SpecimenOrObservationBase
> merge(List
<SpecimenOrObservationBase
> arg0
) {
1014 return defaultService
.merge(arg0
);
1018 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(java.util.UUID, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
1021 public DeleteResult
deleteDerivateHierarchy(UUID arg0
, SpecimenDeleteConfigurator arg1
) {
1022 return defaultService
.deleteDerivateHierarchy(arg0
, arg1
);
1026 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteSingleRead(java.util.UUID, java.util.UUID)
1029 public DeleteResult
deleteSingleRead(UUID arg0
, UUID arg1
) {
1030 return defaultService
.deleteSingleRead(arg0
, arg1
);
1034 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#moveDerivate(java.util.UUID, java.util.UUID, java.util.UUID)
1037 public UpdateResult
moveDerivate(UUID arg0
, UUID arg1
, UUID arg2
) {
1038 return defaultService
.moveDerivate(arg0
, arg1
, arg2
);
1042 * @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)
1045 public boolean moveDerivate(SpecimenOrObservationBase
<?
> from
, SpecimenOrObservationBase
<?
> to
, DerivedUnit derivate
) {
1046 return defaultService
.moveDerivate(from
, to
, derivate
);
1050 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#moveSequence(java.util.UUID, java.util.UUID, java.util.UUID)
1053 public UpdateResult
moveSequence(UUID arg0
, UUID arg1
, UUID arg2
) {
1054 return defaultService
.moveSequence(arg0
, arg1
, arg2
);
1058 public Pager
<Media
> getMediainHierarchy(SpecimenOrObservationBase arg0
, Integer arg1
, Integer arg2
,
1059 List
<String
> arg3
) {
1060 return defaultService
.getMediainHierarchy(arg0
, arg1
, arg2
, arg3
);
1064 * @see eu.etaxonomy.cdm.api.service.IService#merge(java.util.List, boolean)
1067 public List
<MergeResult
<SpecimenOrObservationBase
>> merge(List
<SpecimenOrObservationBase
> arg0
, boolean arg1
) {
1068 return defaultService
.merge(arg0
, arg1
);
1072 * @see eu.etaxonomy.cdm.api.service.IService#merge(eu.etaxonomy.cdm.model.common.ICdmBase, boolean)
1075 public MergeResult
<SpecimenOrObservationBase
> merge(SpecimenOrObservationBase arg0
, boolean arg1
) {
1076 return defaultService
.merge(arg0
, arg1
);
1083 public Collection
<TaxonBase
<?
>> listAssociatedTaxa(SpecimenOrObservationBase
<?
> arg0
, Integer arg1
, Integer arg2
,
1084 List
<OrderHint
> arg3
, List
<String
> arg4
) {
1085 return defaultService
.listAssociatedTaxa(arg0
, arg1
, arg2
, arg3
, arg4
);