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
.config
.DeleteConfiguratorBase
;
33 import eu
.etaxonomy
.cdm
.api
.service
.config
.IIdentifiableEntityServiceConfigurator
;
34 import eu
.etaxonomy
.cdm
.api
.service
.config
.SpecimenDeleteConfigurator
;
35 import eu
.etaxonomy
.cdm
.api
.service
.dto
.DerivateHierarchyDTO
;
36 import eu
.etaxonomy
.cdm
.api
.service
.dto
.FindByIdentifierDTO
;
37 import eu
.etaxonomy
.cdm
.api
.service
.pager
.Pager
;
38 import eu
.etaxonomy
.cdm
.api
.service
.search
.SearchResult
;
39 import eu
.etaxonomy
.cdm
.api
.service
.util
.TaxonRelationshipEdge
;
40 import eu
.etaxonomy
.cdm
.common
.monitor
.IProgressMonitor
;
41 import eu
.etaxonomy
.cdm
.model
.common
.Annotation
;
42 import eu
.etaxonomy
.cdm
.model
.common
.CdmBase
;
43 import eu
.etaxonomy
.cdm
.model
.common
.DefinedTerm
;
44 import eu
.etaxonomy
.cdm
.model
.common
.ICdmBase
;
45 import eu
.etaxonomy
.cdm
.model
.common
.ISourceable
;
46 import eu
.etaxonomy
.cdm
.model
.common
.IdentifiableSource
;
47 import eu
.etaxonomy
.cdm
.model
.common
.LSID
;
48 import eu
.etaxonomy
.cdm
.model
.common
.Language
;
49 import eu
.etaxonomy
.cdm
.model
.common
.Marker
;
50 import eu
.etaxonomy
.cdm
.model
.common
.MarkerType
;
51 import eu
.etaxonomy
.cdm
.model
.common
.UuidAndTitleCache
;
52 import eu
.etaxonomy
.cdm
.model
.description
.DescriptionBase
;
53 import eu
.etaxonomy
.cdm
.model
.description
.IndividualsAssociation
;
54 import eu
.etaxonomy
.cdm
.model
.location
.Country
;
55 import eu
.etaxonomy
.cdm
.model
.media
.Media
;
56 import eu
.etaxonomy
.cdm
.model
.media
.Rights
;
57 import eu
.etaxonomy
.cdm
.model
.molecular
.DnaSample
;
58 import eu
.etaxonomy
.cdm
.model
.molecular
.Sequence
;
59 import eu
.etaxonomy
.cdm
.model
.name
.SpecimenTypeDesignation
;
60 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivationEvent
;
61 import eu
.etaxonomy
.cdm
.model
.occurrence
.DerivedUnit
;
62 import eu
.etaxonomy
.cdm
.model
.occurrence
.DeterminationEvent
;
63 import eu
.etaxonomy
.cdm
.model
.occurrence
.FieldUnit
;
64 import eu
.etaxonomy
.cdm
.model
.occurrence
.SpecimenOrObservationBase
;
65 import eu
.etaxonomy
.cdm
.model
.taxon
.Taxon
;
66 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonBase
;
67 import eu
.etaxonomy
.cdm
.model
.view
.AuditEvent
;
68 import eu
.etaxonomy
.cdm
.model
.view
.AuditEventRecord
;
69 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.AuditEventSort
;
70 import eu
.etaxonomy
.cdm
.persistence
.query
.Grouping
;
71 import eu
.etaxonomy
.cdm
.persistence
.query
.MatchMode
;
72 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
;
73 import eu
.etaxonomy
.cdm
.strategy
.cache
.common
.IIdentifiableEntityCacheStrategy
;
74 import eu
.etaxonomy
.cdm
.strategy
.match
.IMatchStrategy
;
75 import eu
.etaxonomy
.cdm
.strategy
.merge
.IMergeStrategy
;
82 public class TransientOccurenceService
implements IOccurrenceService
{
84 private final IOccurrenceService defaultService
;
85 private final Collection
<SpecimenOrObservationBase
<?
>> units
;
88 * @param defaultService
90 public TransientOccurenceService(IOccurrenceService defaultService
) {
91 this.defaultService
= defaultService
;
92 this.units
= new HashSet
<SpecimenOrObservationBase
<?
>>();
100 * @param propertyPaths
102 * @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)
105 public Pager
<AuditEventRecord
<SpecimenOrObservationBase
>> pageAuditEvents(SpecimenOrObservationBase t
, Integer pageSize
, Integer pageNumber
, AuditEventSort sort
, List
<String
> propertyPaths
) {
106 return defaultService
.pageAuditEvents(t
, pageSize
, pageNumber
, sort
, propertyPaths
);
110 * @param annotatedObj
115 * @param propertyPaths
117 * @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)
120 public Pager
<Annotation
> getAnnotations(SpecimenOrObservationBase annotatedObj
, MarkerType status
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
121 return defaultService
.getAnnotations(annotatedObj
, status
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
126 * @see eu.etaxonomy.cdm.api.service.IService#clear()
129 public void clear() {
130 defaultService
.clear();
136 * @see eu.etaxonomy.cdm.api.service.IService#lock(eu.etaxonomy.cdm.model.common.ICdmBase, org.hibernate.LockMode)
139 public void lock(SpecimenOrObservationBase t
, LockOptions lockOptions
) {
140 defaultService
.lock(t
, lockOptions
);
146 * @param propertyPaths
147 * @see eu.etaxonomy.cdm.api.service.IService#refresh(eu.etaxonomy.cdm.model.common.ICdmBase, org.hibernate.LockMode, java.util.List)
150 public void refresh(SpecimenOrObservationBase t
, LockOptions lockOptions
, List
<String
> propertyPaths
) {
151 defaultService
.refresh(t
, lockOptions
, propertyPaths
);
156 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#updateTitleCache()
159 public void updateTitleCache() {
160 defaultService
.updateTitleCache();
166 * @see eu.etaxonomy.cdm.api.service.IVersionableService#getNextAuditEvent(eu.etaxonomy.cdm.model.common.VersionableEntity)
169 public AuditEventRecord
<SpecimenOrObservationBase
> getNextAuditEvent(SpecimenOrObservationBase t
) {
170 return defaultService
.getNextAuditEvent(t
);
174 * @param annotatableEntity
179 * @param propertyPaths
181 * @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)
184 public Pager
<Marker
> getMarkers(SpecimenOrObservationBase annotatableEntity
, Boolean technical
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
185 return defaultService
.getMarkers(annotatableEntity
, technical
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
191 * @param cacheStrategy
193 * @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)
196 public void updateTitleCache(Class
<?
extends SpecimenOrObservationBase
> clazz
, Integer stepSize
, IIdentifiableEntityCacheStrategy
<SpecimenOrObservationBase
> cacheStrategy
, IProgressMonitor monitor
) {
197 defaultService
.updateTitleCache(clazz
, stepSize
, cacheStrategy
, monitor
);
203 * @see eu.etaxonomy.cdm.api.service.IVersionableService#getPreviousAuditEvent(eu.etaxonomy.cdm.model.common.VersionableEntity)
206 public AuditEventRecord
<SpecimenOrObservationBase
> getPreviousAuditEvent(SpecimenOrObservationBase t
) {
207 return defaultService
.getPreviousAuditEvent(t
);
213 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getCountryByIso(java.lang.String)
216 public Country
getCountryByIso(String iso639
) {
217 return defaultService
.getCountryByIso(iso639
);
223 * @see eu.etaxonomy.cdm.api.service.IService#count(java.lang.Class)
226 public int count(Class
<?
extends SpecimenOrObservationBase
> clazz
) {
227 return defaultService
.count(clazz
);
233 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getCountryByName(java.lang.String)
236 public List
<Country
> getCountryByName(String name
) {
237 return defaultService
.getCountryByName(name
);
242 * @param determinedAs
246 * @param propertyPaths
248 * @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)
251 public Pager
<SpecimenOrObservationBase
> list(Class
<?
extends SpecimenOrObservationBase
> type
, TaxonBase determinedAs
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
252 return defaultService
.list(type
, determinedAs
, limit
, start
, orderHints
, propertyPaths
);
263 * @param propertyPaths
265 * @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)
268 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
) {
269 return defaultService
.pageAuditEvents(clazz
, from
, to
, criteria
, pageSize
, pageValue
, sort
, propertyPaths
);
275 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#find(eu.etaxonomy.cdm.model.common.LSID)
278 public SpecimenOrObservationBase
find(LSID lsid
) {
279 return defaultService
.find(lsid
);
283 * @param persistentObject
285 * @see eu.etaxonomy.cdm.api.service.IService#delete(eu.etaxonomy.cdm.model.common.ICdmBase)
288 public DeleteResult
delete(SpecimenOrObservationBase persistentObject
) {
289 return defaultService
.delete(persistentObject
);
297 * @param propertyPaths
299 * @see eu.etaxonomy.cdm.api.service.IAnnotatableService#groupMarkers(java.lang.Class, java.lang.Boolean, java.lang.Integer, java.lang.Integer, java.util.List)
302 public List
<Object
[]> groupMarkers(Class
<?
extends SpecimenOrObservationBase
> clazz
, Boolean technical
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
303 return defaultService
.groupMarkers(clazz
, technical
, pageSize
, pageNumber
, propertyPaths
);
309 * @see eu.etaxonomy.cdm.api.service.IService#exists(java.util.UUID)
312 public boolean exists(UUID uuid
) {
313 return defaultService
.exists(uuid
);
320 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#replace(eu.etaxonomy.cdm.model.common.IdentifiableEntity, eu.etaxonomy.cdm.model.common.IdentifiableEntity)
323 public SpecimenOrObservationBase
replace(SpecimenOrObservationBase x
, SpecimenOrObservationBase y
) {
324 return defaultService
.replace(x
, y
);
330 * @see eu.etaxonomy.cdm.api.service.IService#find(java.util.Set)
333 public List
<SpecimenOrObservationBase
> find(Set
<UUID
> uuidSet
) {
334 return defaultService
.find(uuidSet
);
341 * @param propertyPaths
343 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getSources(eu.etaxonomy.cdm.model.common.IdentifiableEntity, java.lang.Integer, java.lang.Integer, java.util.List)
346 public Pager
<IdentifiableSource
> getSources(SpecimenOrObservationBase t
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
347 return defaultService
.getSources(t
, pageSize
, pageNumber
, propertyPaths
);
353 * @see eu.etaxonomy.cdm.api.service.IService#find(java.util.UUID)
356 public SpecimenOrObservationBase
find(UUID uuid
) {
357 return defaultService
.find(uuid
);
363 * @see eu.etaxonomy.cdm.api.service.IService#find(int)
366 public SpecimenOrObservationBase
find(int id
) {
367 return defaultService
.find(id
);
374 * @param propertyPaths
376 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getRights(eu.etaxonomy.cdm.model.common.IdentifiableEntity, java.lang.Integer, java.lang.Integer, java.util.List)
379 public Pager
<Rights
> getRights(SpecimenOrObservationBase t
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
380 return defaultService
.getRights(t
, pageSize
, pageNumber
, propertyPaths
);
387 * @see eu.etaxonomy.cdm.api.service.IAnnotatableService#countMarkers(java.lang.Class, java.lang.Boolean)
390 public int countMarkers(Class
<?
extends SpecimenOrObservationBase
> clazz
, Boolean technical
) {
391 return defaultService
.countMarkers(clazz
, technical
);
398 * @param propertyPaths
400 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getMedia(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List)
403 public Pager
<Media
> getMedia(SpecimenOrObservationBase occurence
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
404 return defaultService
.getMedia(occurence
, pageSize
, pageNumber
, propertyPaths
);
410 * @see eu.etaxonomy.cdm.api.service.IService#findById(java.util.Set)
413 public List
<SpecimenOrObservationBase
> findById(Set
<Integer
> idSet
) {
414 return defaultService
.findById(idSet
);
422 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getSourcedObjectByIdInSource(java.lang.Class, java.lang.String, java.lang.String)
425 public ISourceable
getSourcedObjectByIdInSource(Class clazz
, String idInSource
, String idNamespace
) {
426 return defaultService
.getSourcedObjectByIdInSource(clazz
, idInSource
, idNamespace
);
431 * @see eu.etaxonomy.cdm.api.service.IService#getSession()
434 public Session
getSession() {
435 return defaultService
.getSession();
440 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#getUuidAndTitleCache()
443 public List
<UuidAndTitleCache
<SpecimenOrObservationBase
>> getUuidAndTitleCache() {
444 return defaultService
.getUuidAndTitleCache();
452 * @param propertyPaths
454 * @see eu.etaxonomy.cdm.api.service.IService#group(java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
457 public List
<Object
[]> group(Class
<?
extends SpecimenOrObservationBase
> clazz
, Integer limit
, Integer start
, List
<Grouping
> groups
, List
<String
> propertyPaths
) {
458 return defaultService
.group(clazz
, limit
, start
, groups
, propertyPaths
);
466 * @param propertyPaths
468 * @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)
471 public Pager
<DeterminationEvent
> getDeterminations(SpecimenOrObservationBase occurence
, TaxonBase taxonBase
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
472 return defaultService
.getDeterminations(occurence
, taxonBase
, pageSize
, pageNumber
, propertyPaths
);
483 * @param propertyPaths
485 * @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)
488 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
) {
489 return defaultService
.findByTitle(clazz
, queryString
, matchmode
, criteria
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
496 * @param propertyPaths
498 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivationEvents(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List)
501 public Pager
<DerivationEvent
> getDerivationEvents(SpecimenOrObservationBase occurence
, Integer pageSize
, Integer pageNumber
, List
<String
> propertyPaths
) {
502 return defaultService
.getDerivationEvents(occurence
, pageSize
, pageNumber
, propertyPaths
);
510 * @param propertyPaths
512 * @see eu.etaxonomy.cdm.api.service.IService#list(java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
515 public <S
extends SpecimenOrObservationBase
> List
<S
> list(Class
<S
> type
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
516 return defaultService
.list(type
, limit
, start
, orderHints
, propertyPaths
);
525 * @param propertyPaths
527 * @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)
530 public Pager
<SpecimenOrObservationBase
> search(Class
<?
extends SpecimenOrObservationBase
> clazz
, String query
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
531 return defaultService
.search(clazz
, query
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
535 * @param configurator
537 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#findByTitle(eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator)
540 public Pager
<SpecimenOrObservationBase
> findByTitle(IIdentifiableEntityServiceConfigurator
<SpecimenOrObservationBase
> configurator
) {
541 return defaultService
.findByTitle(configurator
);
550 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#countByTitle(java.lang.Class, java.lang.String, eu.etaxonomy.cdm.persistence.query.MatchMode, java.util.List)
553 public Integer
countByTitle(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, MatchMode matchmode
, List
<Criterion
> criteria
) {
554 return defaultService
.countByTitle(clazz
, queryString
, matchmode
, criteria
);
560 * @see eu.etaxonomy.cdm.api.service.IService#load(java.util.UUID)
563 public SpecimenOrObservationBase
load(UUID uuid
) {
564 return defaultService
.load(uuid
);
569 * @param propertyPaths
571 * @see eu.etaxonomy.cdm.api.service.IService#load(java.util.UUID, java.util.List)
574 public SpecimenOrObservationBase
load(UUID uuid
, List
<String
> propertyPaths
) {
575 return defaultService
.load(uuid
, propertyPaths
);
579 * @param configurator
581 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#countByTitle(eu.etaxonomy.cdm.api.service.config.IIdentifiableEntityServiceConfigurator)
584 public Integer
countByTitle(IIdentifiableEntityServiceConfigurator
<SpecimenOrObservationBase
> configurator
) {
585 return defaultService
.countByTitle(configurator
);
590 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnitUuidAndTitleCache()
593 public List
<UuidAndTitleCache
<FieldUnit
>> getFieldUnitUuidAndTitleCache() {
594 return defaultService
.getFieldUnitUuidAndTitleCache();
599 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitUuidAndTitleCache()
602 public List
<UuidAndTitleCache
<DerivedUnit
>> getDerivedUnitUuidAndTitleCache() {
603 return defaultService
.getDerivedUnitUuidAndTitleCache();
607 * @param transientObject
609 * @see eu.etaxonomy.cdm.api.service.IService#merge(eu.etaxonomy.cdm.model.common.ICdmBase)
612 public SpecimenOrObservationBase
merge(SpecimenOrObservationBase transientObject
) {
613 return defaultService
.merge(transientObject
);
618 * @param propertyPaths
620 * @throws DerivedUnitFacadeNotSupportedException
621 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getDerivedUnitFacade(eu.etaxonomy.cdm.model.occurrence.DerivedUnit, java.util.List)
624 public DerivedUnitFacade
getDerivedUnitFacade(DerivedUnit derivedUnit
, List
<String
> propertyPaths
) throws DerivedUnitFacadeNotSupportedException
{
625 return defaultService
.getDerivedUnitFacade(derivedUnit
, propertyPaths
);
636 * @param propertyPaths
638 * @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)
641 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
) {
642 return defaultService
.listByTitle(clazz
, queryString
, matchmode
, criteria
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
647 * @param propertyPaths
649 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDerivedUnitFacades(eu.etaxonomy.cdm.model.description.DescriptionBase, java.util.List)
652 public List
<DerivedUnitFacade
> listDerivedUnitFacades(DescriptionBase description
, List
<String
> propertyPaths
) {
653 return defaultService
.listDerivedUnitFacades(description
, propertyPaths
);
661 * @param propertyPaths
663 * @see eu.etaxonomy.cdm.api.service.IService#page(java.lang.Class, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
666 public <S
extends SpecimenOrObservationBase
> Pager
<S
> page(Class
<S
> type
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
667 return defaultService
.page(type
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
672 * @param includeRelationships
673 * @param associatedTaxon
678 * @param propertyPaths
680 * @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)
683 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
) {
684 return defaultService
.listByAssociatedTaxon(type
, includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
688 * @param persistentObject
690 * @see eu.etaxonomy.cdm.api.service.IService#refresh(eu.etaxonomy.cdm.model.common.ICdmBase)
693 public UUID
refresh(SpecimenOrObservationBase persistentObject
) {
694 return defaultService
.refresh(persistentObject
);
705 * @param propertyPaths
707 * @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)
710 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
) {
711 return defaultService
.listByReferenceTitle(clazz
, queryString
, matchmode
, criteria
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
719 * @see eu.etaxonomy.cdm.api.service.IService#rows(java.lang.String, int, int)
722 public List
<SpecimenOrObservationBase
> rows(String tableName
, int limit
, int start
) {
723 return defaultService
.rows(tableName
, limit
, start
);
727 * @param newInstances
729 * @see eu.etaxonomy.cdm.api.service.IService#save(java.util.Collection)
732 public Map
<UUID
, SpecimenOrObservationBase
> save(Collection
<SpecimenOrObservationBase
> newInstances
) {
733 for(SpecimenOrObservationBase unit
:newInstances
){
741 * @param includeRelationships
742 * @param associatedTaxon
747 * @param propertyPaths
749 * @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)
752 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
) {
753 return defaultService
.pageByAssociatedTaxon(type
, includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
759 * @see eu.etaxonomy.cdm.api.service.IService#save(eu.etaxonomy.cdm.model.common.ICdmBase)
762 public UUID
save(SpecimenOrObservationBase newInstance
) {
763 units
.add(newInstance
);
768 * @param transientObject
770 * @see eu.etaxonomy.cdm.api.service.IService#saveOrUpdate(eu.etaxonomy.cdm.model.common.ICdmBase)
773 public UUID
saveOrUpdate(SpecimenOrObservationBase transientObject
) {
774 units
.add(transientObject
);
779 * @param transientObjects
781 * @see eu.etaxonomy.cdm.api.service.IService#saveOrUpdate(java.util.Collection)
784 public Map
<UUID
, SpecimenOrObservationBase
> saveOrUpdate(Collection
<SpecimenOrObservationBase
> transientObjects
) {
785 for(SpecimenOrObservationBase unit
:transientObjects
){
796 * @param highlightFragments
800 * @param propertyPaths
802 * @throws CorruptIndexException
803 * @throws IOException
804 * @throws ParseException
805 * @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)
808 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
{
809 return defaultService
.findByFullText(clazz
, queryString
, boundingBox
, languages
, highlightFragments
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
813 * @param transientObject
815 * @see eu.etaxonomy.cdm.api.service.IService#update(eu.etaxonomy.cdm.model.common.ICdmBase)
818 public UUID
update(SpecimenOrObservationBase transientObject
) {
819 return defaultService
.update(transientObject
);
824 * @param includeProperties
828 * @param propertyPaths
830 * @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)
833 public List
<SpecimenOrObservationBase
> list(SpecimenOrObservationBase example
, Set
<String
> includeProperties
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
834 return defaultService
.list(example
, includeProperties
, limit
, start
, orderHints
, propertyPaths
);
839 * @param matchStrategy
840 * @param mergeStrategy
842 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#deduplicate(java.lang.Class, eu.etaxonomy.cdm.strategy.match.IMatchStrategy, eu.etaxonomy.cdm.strategy.merge.IMergeStrategy)
845 public int deduplicate(Class
<?
extends SpecimenOrObservationBase
> clazz
, IMatchStrategy matchStrategy
, IMergeStrategy mergeStrategy
) {
846 return defaultService
.deduplicate(clazz
, matchStrategy
, mergeStrategy
);
857 * @see eu.etaxonomy.cdm.api.service.IIdentifiableEntityService#findTitleCache(java.lang.Class, java.lang.String, java.lang.Integer, java.lang.Integer, java.util.List, eu.etaxonomy.cdm.persistence.query.MatchMode)
860 public Pager
<SpecimenOrObservationBase
> findTitleCache(Class
<?
extends SpecimenOrObservationBase
> clazz
, String queryString
, Integer pageSize
, Integer pageNumber
, List
<OrderHint
> orderHints
, MatchMode matchMode
) {
861 return defaultService
.findTitleCache(clazz
, queryString
, pageSize
, pageNumber
, orderHints
, matchMode
);
867 public Collection
<SpecimenOrObservationBase
<?
>> getUnits() {
872 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#getFieldUnits(java.util.UUID)
875 public Collection
<FieldUnit
> getFieldUnits(UUID derivedUnitUuid
) {
876 return defaultService
.getFieldUnits(derivedUnitUuid
);
880 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#pageByAssociatedTaxon(java.lang.Class, java.util.Set, java.lang.String, java.lang.Integer, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
883 public <T
extends SpecimenOrObservationBase
> Pager
<T
> pageByAssociatedTaxon(Class
<T
> type
,
884 Set
<TaxonRelationshipEdge
> includeRelationships
, String taxonUUID
, Integer maxDepth
, Integer pageSize
,
885 Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
886 return defaultService
.pageByAssociatedTaxon(type
, includeRelationships
, taxonUUID
,
887 maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
891 * @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)
894 public boolean moveDerivate(SpecimenOrObservationBase
<?
> from
, SpecimenOrObservationBase
<?
> to
, DerivedUnit derivate
) {
895 return defaultService
.moveDerivate(from
, to
, derivate
);
899 * @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)
902 public boolean moveSequence(DnaSample from
, DnaSample to
, Sequence sequence
) {
903 return defaultService
.moveSequence(from
, to
, sequence
);
907 public DeleteResult
isDeletable(SpecimenOrObservationBase object
,
908 DeleteConfiguratorBase config
) {
909 return defaultService
.isDeletable(object
, config
);
913 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#countDeterminations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.model.taxon.TaxonBase)
916 public int countDeterminations(SpecimenOrObservationBase occurence
, TaxonBase taxonbase
) {
917 return defaultService
.countDeterminations(occurence
, taxonbase
);
921 public SpecimenOrObservationBase
findWithoutFlush(UUID uuid
) {
922 return defaultService
.findWithoutFlush(uuid
);
926 public Collection
<SpecimenOrObservationBase
> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon
,
927 List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
928 return defaultService
.listFieldUnitsByAssociatedTaxon(associatedTaxon
, orderHints
, propertyPaths
);
932 public Pager
<SpecimenOrObservationBase
> pageFieldUnitsByAssociatedTaxon(
933 Set
<TaxonRelationshipEdge
> includeRelationships
, Taxon associatedTaxon
, Integer maxDepth
, Integer pageSize
,
934 Integer pageNumber
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
935 return defaultService
.pageFieldUnitsByAssociatedTaxon(includeRelationships
, associatedTaxon
, maxDepth
, pageSize
, pageNumber
, orderHints
, propertyPaths
);
940 public DerivateHierarchyDTO
assembleDerivateHierarchyDTO(FieldUnit fieldUnit
, UUID associatedTaxonUuid
) {
941 return defaultService
.assembleDerivateHierarchyDTO(fieldUnit
, associatedTaxonUuid
);
945 public Collection
<ICdmBase
> getNonCascadedAssociatedElements(SpecimenOrObservationBase
<?
> specimen
) {
946 return defaultService
.getNonCascadedAssociatedElements(specimen
);
950 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#deleteDerivateHierarchy(eu.etaxonomy.cdm.model.common.ICdmBase)
953 public DeleteResult
deleteDerivateHierarchy(CdmBase from
, SpecimenDeleteConfigurator config
) {
954 return defaultService
.deleteDerivateHierarchy(from
, config
);
958 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#delete(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator)
961 public DeleteResult
delete(SpecimenOrObservationBase
<?
> specimen
, SpecimenDeleteConfigurator config
) {
962 return defaultService
.delete(specimen
, config
);
966 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listIndividualsAssociations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
969 public Collection
<IndividualsAssociation
> listIndividualsAssociations(SpecimenOrObservationBase
<?
> specimen
,
970 Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
971 return defaultService
.listIndividualsAssociations(specimen
, limit
, start
, orderHints
, propertyPaths
);
975 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listTypeDesignations(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
978 public Collection
<SpecimenTypeDesignation
> listTypeDesignations(SpecimenOrObservationBase
<?
> specimen
,
979 Integer limit
, Integer start
, List
<OrderHint
> orderHints
, List
<String
> propertyPaths
) {
980 return defaultService
.listTypeDesignations(specimen
, limit
, start
, orderHints
, propertyPaths
);
984 * @see eu.etaxonomy.cdm.api.service.IOccurrenceService#listDescriptionsWithDescriptionSpecimen(eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase, java.lang.Integer, java.lang.Integer, java.util.List, java.util.List)
987 public Collection
<DescriptionBase
<?
>> listDescriptionsWithDescriptionSpecimen(
988 SpecimenOrObservationBase
<?
> specimen
, Integer limit
, Integer start
, List
<OrderHint
> orderHints
,
989 List
<String
> propertyPaths
) {
990 return defaultService
.listDescriptionsWithDescriptionSpecimen(specimen
, limit
, start
, orderHints
, propertyPaths
);
994 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
){
995 return defaultService
.findByIdentifier(clazz
, identifier
, identifierType
, matchmode
, includeEntity
, pageSize
, pageNumber
, propertyPaths
);