public interface IOccurrenceService extends IIdentifiableEntityService<SpecimenOrObservationBase>
Modifier and Type | Method and Description |
---|---|
FieldUnitDTO |
assembleFieldUnitDTO(FieldUnit fieldUnit)
Assembles a
FieldUnitDTO for the given field unit. |
PreservedSpecimenDTO |
assemblePreservedSpecimenDTO(DerivedUnit derivedUnit)
Assembles a
PreservedSpecimenDTO for the given derived unit. |
long |
countDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonbase)
Returns a count of determinations that have been made for a given occurence and for a given taxon concept
|
long |
countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config)
Returns the number of specimens that match the given parameters
NOTE - issue #6484: the parameters FindOccurrencesConfigurator.getAssignmentStatus()
and FindOccurrencesConfigurator.isRetrieveIndirectlyAssociatedSpecimens() are not evaluated
in the count method |
DeleteResult |
delete(SpecimenOrObservationBase<?> specimen,
SpecimenDeleteConfigurator config)
Deletes the specified specimen according to the setting in the
SpecimenDeleteConfigurator . |
DeleteResult |
delete(java.util.UUID specimenUuid,
SpecimenDeleteConfigurator config)
Deletes the specified specimen belonging to the given
UUID
according to the setting in the SpecimenDeleteConfigurator . |
FieldUnitDTO |
findByAccessionNumber(java.lang.String accessionNumberString,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
Pager<SearchResult<SpecimenOrObservationBase>> |
findByFullText(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
java.lang.String queryString,
org.hibernate.search.spatial.impl.Rectangle boundingBox,
java.util.List<Language> languages,
boolean highlightFragments,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<PreservedSpecimenDTO> |
findByTitlePreservedSpecimenDTO(FindOccurrencesConfigurator config)
Returns a list of
PreservedSpecimenDTO for the specimens found with the
given configurator |
Pager<UuidAndTitleCache<SpecimenOrObservationBase>> |
findByTitleUuidAndTitleCache(FindOccurrencesConfigurator config)
Returns a list of
UuidAndTitleCache for the specimens found with the
given configurator |
FieldUnitDTO |
findFieldUnitDTO(DerivateDTO derivedUnitDTO,
java.util.Collection<FieldUnitDTO> fieldUnits,
java.util.HashMap<java.util.UUID,DerivateDTO> alreadyCollectedSpecimen) |
java.util.List<FieldUnitDTO> |
findFieldUnitDTOByAssociatedTaxon(java.util.Set<TaxonRelationshipEdge> includedRelationships,
java.util.UUID associatedTaxonUuid) |
java.util.Collection<FieldUnit> |
findFieldUnits(java.util.UUID specimenUuid,
java.util.List<java.lang.String> propertyPaths)
|
java.util.List<FieldUnit> |
findFieldUnitsForGatheringEvent(java.util.UUID gatheringEventUuid)
Returns all
FieldUnit s that are referencing this GatheringEvent |
java.util.List<Point> |
findPointsForFieldUnitList(java.util.List<java.util.UUID> fieldUnitUuids) |
java.util.List<DerivedUnit> |
getAllChildDerivatives(SpecimenOrObservationBase<?> specimen)
Returns all child derivatives of the given specimen.
|
java.util.List<DerivedUnit> |
getAllChildDerivatives(java.util.UUID specimenUuid)
Returns all child derivatives of the given specimen.
|
java.util.List<SpecimenOrObservationBase<?>> |
getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen)
Return the all
SpecimenOrObservationBase s of the complete
derivative hierarchy i.e. |
java.util.Collection<DescriptionElementBase> |
getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen)
Gets all description elements that are used for describing the character
states of the given specimen
|
java.util.Collection<DescriptionElementBase> |
getCharacterDataForSpecimen(java.util.UUID specimenUuid)
Gets all description elements that are used for describing the character
states of the given specimen
|
Country |
getCountryByIso(java.lang.String iso639) |
java.util.List<Country> |
getCountryByName(java.lang.String name) |
Pager<DerivationEvent> |
getDerivationEvents(SpecimenOrObservationBase occurence,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of derivation events that have involved creating new DerivedUnits from this occurence
|
DerivedUnitFacade |
getDerivedUnitFacade(DerivedUnit derivedUnit,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<DerivedUnit>> |
getDerivedUnitUuidAndTitleCache(java.lang.Integer limit,
java.lang.String pattern)
Retrieves the
UUID and the string representation (title cache) of all
DerivedUnit s found in the data base. |
Pager<DeterminationEvent> |
getDeterminations(SpecimenOrObservationBase occurence,
TaxonBase taxonBase,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of determinations that have been made for a given occurence
|
java.util.List<UuidAndTitleCache<FieldUnit>> |
getFieldUnitUuidAndTitleCache()
Retrieves the
UUID and the string representation (title cache) of all
FieldUnit s found in the data base. |
Pager<Media> |
getMedia(SpecimenOrObservationBase occurence,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a List of Media that are associated with a given occurence
|
Pager<Media> |
getMediainHierarchy(SpecimenOrObservationBase rootOccurence,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns all media attached to this occurence and its children.
|
java.lang.String |
getMostSignificantIdentifier(DerivedUnit derivedUnit)
Returns the most significant identifier for the given
DerivedUnit . |
Pager<SpecimenOrObservationBase> |
list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonBase determinedAs,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a paged list of occurrences that have been determined to belong
to the taxon concept determinedAs, optionally restricted to objects
belonging to a class that that extends SpecimenOrObservationBase.
|
Pager<SpecimenOrObservationBase> |
list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonName determinedAs,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a paged list of occurrences that have been determined to belong
to the taxon name determinedAs, optionally restricted to objects
belonging to a class that that extends SpecimenOrObservationBase.
|
java.util.Collection<TaxonBase<?>> |
listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all associated taxa for the given specimen (via type designations, determination, individuals associations)
|
java.util.Collection<TaxonBase<?>> |
listAssociatedTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
<T extends SpecimenOrObservationBase> |
listByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Lists all instances of
SpecimenOrObservationBase which are
associated with the taxon specified as parameter. |
java.util.List<DerivedUnitFacade> |
listDerivedUnitFacades(DescriptionBase description,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<DescriptionBase<?>> |
listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
DescriptionBase s that have the given specimen set as described specimen. |
java.util.Collection<DeterminationEvent> |
listDeterminationEvents(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
DeterminationEvent s which have the given specimen set as identified unit. |
java.util.Collection<TaxonBase<?>> |
listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa that the given specimen is determined as
|
java.util.Collection<TaxonBase<?>> |
listDeterminedTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<SpecimenOrObservationBase> |
listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Lists all instances of
FieldUnit which are
associated directly or indirectlywith the taxon specified
as parameter. |
java.util.Collection<IndividualsAssociation> |
listIndividualsAssociations(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
IndividualsAssociation with the given specimen. |
java.util.Collection<TaxonBase<?>> |
listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa linked via
IndividualsAssociation with the given specimen. |
java.util.Map<DerivedUnit,java.util.Collection<SpecimenTypeDesignation>> |
listTypeDesignations(java.util.Collection<DerivedUnit> specimens,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
SpecimenTypeDesignation s which have the given specimens as a type specimen. |
java.util.Collection<SpecimenTypeDesignation> |
listTypeDesignations(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
SpecimenTypeDesignation s which have the given specimen as a type specimen. |
java.util.Collection<TaxonBase<?>> |
listTypeDesignationTaxa(DerivedUnit specimen,
boolean includeUnpublished,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.Collection<TaxonBase<?>> |
listTypeDesignationTaxa(DerivedUnit specimen,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all taxa with a
SpecimenTypeDesignation with the given specimen as a type specimen. |
java.util.Collection<SpecimenNodeWrapper> |
listUuidAndTitleCacheByAssociatedTaxon(java.util.List<java.util.UUID> taxonNodeUuids,
java.lang.Integer limit,
java.lang.Integer start)
The method will search for specimen associated with the taxon nodes.
It will search for 3 possible association types: - via IndividualAssociations of the taxon - via TypeDesignations of the taxon name - via Determinations of the taxon or taxon name more are covered in IIdentifiableEntityService.findByTitle(IIdentifiableEntityServiceConfigurator) |
FieldUnitDTO |
loadFieldUnitDTO(java.util.UUID derivedUnitUuid)
Load the FieldUnitDTO for the given
derivedUnitUuid with all intermediate derivatives and GatheringEventDTO |
boolean |
moveDerivate(SpecimenOrObservationBase<?> from,
SpecimenOrObservationBase<?> to,
DerivedUnit derivate) |
UpdateResult |
moveDerivate(java.util.UUID specimenFromUuid,
java.util.UUID specimenToUuid,
java.util.UUID derivateUuid)
Moves the given
DerivedUnit from one SpecimenOrObservationBase to another. |
UpdateResult |
moveSequence(DnaSample from,
DnaSample to,
Sequence sequence)
|
UpdateResult |
moveSequence(java.util.UUID fromUuid,
java.util.UUID toUuid,
java.util.UUID sequenceUuid) |
<T extends SpecimenOrObservationBase> |
pageByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
java.lang.String taxonUUID,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
See
#listByAssociatedTaxon(Class, Set, String, Integer, Integer, Integer, List, List) |
<T extends SpecimenOrObservationBase> |
pageByAssociatedTaxon(java.lang.Class<T> type,
java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
|
Pager<SpecimenOrObservationBase> |
pageFieldUnitsByAssociatedTaxon(java.util.Set<TaxonRelationshipEdge> includeRelationships,
Taxon associatedTaxon,
java.lang.Integer maxDepth,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
See
#listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List) |
Pager<SpecimenOrObservationBase> |
search(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
java.lang.String query,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a Paged List of SpecimenOrObservationBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
countByTitle, countByTitle, countByTitleWithRestrictions, deduplicate, find, findByIdentifier, findByMarker, findByTitle, findByTitle, findByTitleWithRestrictions, findTitleCache, findUuidAndTitleCacheByMarker, getRights, getSourcedObjectByIdInSource, getSources, getTitleCache, getUuidAndTitleCache, getUuidAndTitleCache, listByIdentifier, listByReferenceTitle, listByReferenceTitleWithRestrictions, listByTitle, listByTitleWithRestrictions, replace, updateCaches, updateCaches
countMarkers, getAnnotations, getMarkers, groupMarkers
getNextAuditEvent, getPreviousAuditEvent, isDeletable, pageAuditEvents, pageAuditEvents
clear, count, delete, delete, delete, exists, find, find, find, find, findById, findWithoutFlush, getSession, group, list, list, load, load, load, load, loadByIds, loadByIds, loadWithUpdate, lock, merge, merge, merge, merge, page, page, page, pageByParamWithRestrictions, refresh, refresh, save, save, saveOrUpdate, saveOrUpdate, update
Country getCountryByIso(java.lang.String iso639)
java.util.List<Country> getCountryByName(java.lang.String name)
Pager<SpecimenOrObservationBase> list(java.lang.Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
In contrast to #listByAnyAssociation(Class, Taxon, List)
this
method only takes SpecimenOrObservationBase instances into account which
are actually determined as the taxon specified by
determinedAs
.
type
- The type of entities to return (can be null to count all
entities of type determinedAs
- the taxon concept that the occurrences have been determined to
belong topageSize
- The maximum number of objects returned (can be null for all
matching objects)pageNumber
- The offset (in pageSize chunks) from the start of the result
set (0 - based, can be null, equivalent of starting at the
beginning of the recordset)orderHints
- Supports path like orderHints.propertyNames
which
include *-to-one properties like createdBy.username or
authorTeam.persistentTitleCachepropertyPaths
- properties to be initializedPager<SpecimenOrObservationBase> list(java.lang.Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
In contrast to #listByAnyAssociation(Class, Taxon, List)
this
method only takes SpecimenOrObservationBase instances into account which
are actually determined as the taxon specified by
determinedAs
.
type
- The type of entities to return (can be null to count all
entities of type determinedAs
- the taxon name that the occurrences have been determined to
belong topageSize
- The maximum number of objects returned (can be null for all
matching objects)pageNumber
- The offset (in pageSize chunks) from the start of the result
set (0 - based, can be null, equivalent of starting at the
beginning of the recordset)orderHints
- Supports path like orderHints.propertyNames
which
include *-to-one properties like createdBy.username or
authorTeam.persistentTitleCachepropertyPaths
- properties to be initializedPager<Media> getMedia(SpecimenOrObservationBase occurence, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
occurence
- the occurence associated with these mediapageSize
- The maximum number of media returned (can be null for all related media)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)propertyPaths
- properties to initialize - see IBeanInitializer.initialize(Object, List)
Pager<Media> getMediainHierarchy(SpecimenOrObservationBase rootOccurence, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
MediaSpecimen
and molecular images into account.occurence
- the occurence and its children from which the media to getpageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)propertyPaths
- properties to initialize - see IBeanInitializer.initialize(Object, List)
long countDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonbase)
occurence
- the occurence associated with these determinations (can be null for all occurrences)taxonbase
- the taxon concept associated with these determinations (can be null for all taxon concepts)Pager<DeterminationEvent> getDeterminations(SpecimenOrObservationBase occurence, TaxonBase taxonBase, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
occurence
- the occurence associated with these determinations (can be null for all occurrences)taxonbase
- the taxon concept associated with these determinations (can be null for all taxon concepts)pageSize
- The maximum number of determinations returned (can be null for all related determinations)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)Pager<DerivationEvent> getDerivationEvents(SpecimenOrObservationBase occurence, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
occurence
- the occurence that was a source of these derivation eventspageSize
- The maximum number of derivation events returned (can be null for all related derivation events)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)Pager<SpecimenOrObservationBase> search(java.lang.Class<? extends SpecimenOrObservationBase> clazz, java.lang.String query, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
search
in interface IIdentifiableEntityService<SpecimenOrObservationBase>
clazz
- filter the results by class (or pass null to return all SpecimenOrObservationBase instances)queryString
- pageSize
- The maximum number of occurrences returned (can be null for all matching occurrences)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)orderHints
- Supports path like orderHints.propertyNames
which
include *-to-one properties like createdBy.username or
authorTeam.persistentTitleCachepropertyPaths
- properties to be initializedjava.util.List<UuidAndTitleCache<FieldUnit>> getFieldUnitUuidAndTitleCache()
UUID
and the string representation (title cache) of all
FieldUnit
s found in the data base.UuidAndTitleCache
java.util.List<UuidAndTitleCache<DerivedUnit>> getDerivedUnitUuidAndTitleCache(java.lang.Integer limit, java.lang.String pattern)
UUID
and the string representation (title cache) of all
DerivedUnit
s found in the data base.UuidAndTitleCache
DerivedUnitFacade getDerivedUnitFacade(DerivedUnit derivedUnit, java.util.List<java.lang.String> propertyPaths) throws DerivedUnitFacadeNotSupportedException
java.util.List<DerivedUnitFacade> listDerivedUnitFacades(DescriptionBase description, java.util.List<java.lang.String> propertyPaths)
<T extends SpecimenOrObservationBase> java.util.List<T> listByAssociatedTaxon(java.lang.Class<T> type, java.util.Set<TaxonRelationshipEdge> includeRelationships, Taxon associatedTaxon, java.lang.Integer maxDepth, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
SpecimenOrObservationBase
which are
associated with the taxon
specified as parameter.
SpecimenOrObservationBase instances can be associated to taxa in multiple
ways, all these possible relations are taken into account:
IndividualsAssociation
elements in a
TaxonDescription
contain DerivedUnit
sSpecimenTypeDesignation
s may be associated with any
HomotypicalGroup
related to the specific Taxon
.Taxon
may be referenced by the DeterminationEvent
of the SpecimenOrObservationBase
TaxonRelationship
s. If
the parameter includeRelationships
is containing elements,
these according s and
directional information will be used to collect further
SpecimenOrObservationBase
instances found this way.T
- type
- associatedTaxon
- Set
- includeRelationships. TaxonRelationships will not be taken into account if this is NULL
.maxDepth
- TODOpageSize
- pageNumber
- orderHints
- propertyPaths
- java.util.Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(java.util.List<java.util.UUID> taxonNodeUuids, java.lang.Integer limit, java.lang.Integer start)
IIdentifiableEntityService.findByTitle(IIdentifiableEntityServiceConfigurator)
taxonNodeUuids
- a list of UUID
s of the taxon nodeslimit
- start
- SpecimenNodeWrapper
containing the
TaxonNode
and the corresponding UuidAndTitleCache
object for the specimen found for this taxon nodejava.util.Collection<SpecimenOrObservationBase> listFieldUnitsByAssociatedTaxon(Taxon associatedTaxon, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
FieldUnit
which are
associated directly or indirectlywith the taxon
specified
as parameter. "Indirectly" means that a sub derivate of the FieldUnit is
directly associated with the given taxon.
SpecimenOrObservationBase instances can be associated to taxa in multiple
ways, all these possible relations are taken into account:
IndividualsAssociation
elements in a
TaxonDescription
contain DerivedUnit
sSpecimenTypeDesignation
s may be associated with any
HomotypicalGroup
related to the specific Taxon
.Taxon
may be referenced by the DeterminationEvent
of the SpecimenOrObservationBase
TaxonRelationship
s. If
the parameter includeRelationships
is containing elements,
these according s and
directional information will be used to collect further
SpecimenOrObservationBase
instances found this way.T
- type
- associatedTaxon
- Set
- includeRelationships. TaxonRelationships will not be taken into account if this is NULL
.maxDepth
- TODOpageSize
- pageNumber
- orderHints
- propertyPaths
- Pager<SpecimenOrObservationBase> pageFieldUnitsByAssociatedTaxon(java.util.Set<TaxonRelationshipEdge> includeRelationships, Taxon associatedTaxon, java.lang.Integer maxDepth, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
#listFieldUnitsByAssociatedTaxon(Set, Taxon, Integer, Integer, Integer, List, List)
<T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(java.lang.Class<T> type, java.util.Set<TaxonRelationshipEdge> includeRelationships, Taxon associatedTaxon, java.lang.Integer maxDepth, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
type
- includeRelationships
- associatedTaxon
- maxDepth
- pageSize
- pageNumber
- orderHints
- propertyPaths
- java.util.Collection<FieldUnit> findFieldUnits(java.util.UUID specimenUuid, java.util.List<java.lang.String> propertyPaths)
specimenUuid
- the UUID of the specimenpropertyPaths
- the property pathPager<SearchResult<SpecimenOrObservationBase>> findByFullText(java.lang.Class<? extends SpecimenOrObservationBase> clazz, java.lang.String queryString, org.hibernate.search.spatial.impl.Rectangle boundingBox, java.util.List<Language> languages, boolean highlightFragments, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths) throws java.io.IOException, LuceneParseException
clazz
- queryString
- languages
- highlightFragments
- pageSize
- pageNumber
- orderHints
- propertyPaths
- org.apache.lucene.index.CorruptIndexException
java.io.IOException
ParseException
LuceneParseException
<T extends SpecimenOrObservationBase> Pager<T> pageByAssociatedTaxon(java.lang.Class<T> type, java.util.Set<TaxonRelationshipEdge> includeRelationships, java.lang.String taxonUUID, java.lang.Integer maxDepth, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
#listByAssociatedTaxon(Class, Set, String, Integer, Integer, Integer, List, List)
type
- includeRelationships
- associatedTaxon
- maxDepth
- pageSize
- pageNumber
- orderHints
- propertyPaths
- UpdateResult moveSequence(DnaSample from, DnaSample to, Sequence sequence)
from
- the DnaSample from which the sequence will be removedto
- the DnaSample which to which the sequence will be addedsequence
- the Sequence to movetrue
if successfully moved, false
otherwiseUpdateResult moveSequence(java.util.UUID fromUuid, java.util.UUID toUuid, java.util.UUID sequenceUuid)
fromUuid
- toUuid
- sequenceUuid
- UpdateResult moveDerivate(java.util.UUID specimenFromUuid, java.util.UUID specimenToUuid, java.util.UUID derivateUuid)
DerivedUnit
from one SpecimenOrObservationBase
to another.from
- the SpecimenOrObservationBase from which the DerivedUnit will be removedto
- the SpecimenOrObservationBase to which the DerivedUnit will be addedderivate
- the DerivedUnit to movetrue
if successfully moved, false
otherwiseboolean moveDerivate(SpecimenOrObservationBase<?> from, SpecimenOrObservationBase<?> to, DerivedUnit derivate)
from
- to
- derivate
- FieldUnitDTO assembleFieldUnitDTO(FieldUnit fieldUnit)
FieldUnitDTO
for the given field unit.fieldUnit
- PreservedSpecimenDTO assemblePreservedSpecimenDTO(DerivedUnit derivedUnit)
PreservedSpecimenDTO
for the given derived unit.derivedUnit
- DeleteResult delete(SpecimenOrObservationBase<?> specimen, SpecimenDeleteConfigurator config)
SpecimenDeleteConfigurator
.specimen
- the specimen which shoul be deletedconfig
- specifies options if and how the specimen should be deleted like e.g. including all
of its childrenDeleteResult
which holds information about the outcome of this operationDeleteResult delete(java.util.UUID specimenUuid, SpecimenDeleteConfigurator config)
UUID
according to the setting in the SpecimenDeleteConfigurator
.specimen
- the specimen which shoul be deletedconfig
- specifies options if and how the specimen should be deleted
like e.g. including all of its childrenDeleteResult
which holds information about the
outcome of this operationjava.util.Collection<IndividualsAssociation> listIndividualsAssociations(SpecimenOrObservationBase<?> specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
IndividualsAssociation
with the given specimen.specimen
- the specimen for which the associations are retrievedlimit
- start
- orderHints
- propertyPaths
- java.util.Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
IndividualsAssociation
with the given specimen.specimen
- the specimen which is linked to the taxalimit
- start
- orderHints
- propertyPaths
- java.util.Collection<TaxonBase<?>> listIndividualsAssociationTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
java.util.Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
specimen
- limit
- start
- orderHints
- propertyPaths
- java.util.Collection<TaxonBase<?>> listAssociatedTaxa(SpecimenOrObservationBase<?> specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
#listAssociatedTaxa(SpecimenOrObservationBase, Integer, Integer, List, List)axa
java.util.Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, boolean includeUnpublished, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
specimen
- limit
- start
- orderHints
- propertyPaths
- java.util.Collection<TaxonBase<?>> listDeterminedTaxa(SpecimenOrObservationBase<?> specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
java.util.Collection<DeterminationEvent> listDeterminationEvents(SpecimenOrObservationBase<?> specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
DeterminationEvent
s which have the given specimen set as identified unit.specimen
- limit
- start
- orderHints
- propertyPaths
- java.util.Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
SpecimenTypeDesignation
with the given specimen as a type specimen.specimen
- the type specimenspecimen
- limit
- start
- orderHints
- propertyPaths
- java.util.Collection<TaxonBase<?>> listTypeDesignationTaxa(DerivedUnit specimen, boolean includeUnpublished, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
java.util.Map<DerivedUnit,java.util.Collection<SpecimenTypeDesignation>> listTypeDesignations(java.util.Collection<DerivedUnit> specimens, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
SpecimenTypeDesignation
s which have the given specimens as a type specimen.specimens
- the type specimenslimit
- start
- orderHints
- propertyPaths
- java.util.Collection<SpecimenTypeDesignation> listTypeDesignations(DerivedUnit specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
SpecimenTypeDesignation
s which have the given specimen as a type specimen.specimen
- the type specimenlimit
- start
- orderHints
- propertyPaths
- java.util.Collection<DescriptionBase<?>> listDescriptionsWithDescriptionSpecimen(SpecimenOrObservationBase<?> specimen, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
DescriptionBase
s that have the given specimen set as described specimen.specimen
- the described specimenlimit
- start
- orderHints
- propertyPaths
- java.util.Collection<DescriptionElementBase> getCharacterDataForSpecimen(SpecimenOrObservationBase<?> specimen)
specimen
- the specimen for which the character state description
elements should be retrievedjava.util.Collection<DescriptionElementBase> getCharacterDataForSpecimen(java.util.UUID specimenUuid)
specimenUuid
- the specimen UUID
for which the character state description
elements should be retrievedjava.lang.String getMostSignificantIdentifier(DerivedUnit derivedUnit)
DerivedUnit
.derivedUnit
- the derived unit to checklong countOccurrences(IIdentifiableEntityServiceConfigurator<SpecimenOrObservationBase> config)
FindOccurrencesConfigurator.getAssignmentStatus()
and FindOccurrencesConfigurator.isRetrieveIndirectlyAssociatedSpecimens()
are not evaluated
in the count methodclazz
- the class to matchqueryString
- the queryString to matchtype
- the SpecimenOrObservationType
to matchassociatedTaxon
- the taxon these specimens are in any way associated to via
determination, type designations, individuals associations, etc.matchmode
- determines how the query string should be matchedlimit
- the maximum number of entities returned (can be null to return
all entities)start
- orderHints
- Supports path like orderHints.propertyNames
which
include *-to-one properties like createdBy.username or
authorTeam.persistentTitleCachejava.util.List<SpecimenOrObservationBase<?>> getAllHierarchyDerivatives(SpecimenOrObservationBase<?> specimen)
SpecimenOrObservationBase
s of the complete
derivative hierarchy i.e. all parent and child derivatives and the given
specimen itself.specimen
- a specimen or observationjava.util.List<DerivedUnit> getAllChildDerivatives(SpecimenOrObservationBase<?> specimen)
specimen
- a specimen or observationjava.util.List<DerivedUnit> getAllChildDerivatives(java.util.UUID specimenUuid)
specimen
- the UUID of a specimen or observationjava.util.List<FieldUnit> findFieldUnitsForGatheringEvent(java.util.UUID gatheringEventUuid)
FieldUnit
s that are referencing this GatheringEvent
gatheringEventUuid
- the UUID
of the gathering event@Transactional(readOnly=true) Pager<UuidAndTitleCache<SpecimenOrObservationBase>> findByTitleUuidAndTitleCache(FindOccurrencesConfigurator config)
UuidAndTitleCache
for the specimens found with the
given configuratorconfig
- the configurator for the search@Transactional(readOnly=true) java.util.List<PreservedSpecimenDTO> findByTitlePreservedSpecimenDTO(FindOccurrencesConfigurator config)
PreservedSpecimenDTO
for the specimens found with the
given configuratorconfig
- the configurator for the searchPreservedSpecimenDTO
objectFieldUnitDTO findByAccessionNumber(java.lang.String accessionNumberString, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
queryString
- propertyPaths
- java.io.IOException
java.util.List<FieldUnitDTO> findFieldUnitDTOByAssociatedTaxon(java.util.Set<TaxonRelationshipEdge> includedRelationships, java.util.UUID associatedTaxonUuid)
includedRelationships
- associatedTaxon
- maxDepth
- pageSize
- pageNumber
- orderHints
- propertyPaths
- FieldUnitDTO findFieldUnitDTO(DerivateDTO derivedUnitDTO, java.util.Collection<FieldUnitDTO> fieldUnits, java.util.HashMap<java.util.UUID,DerivateDTO> alreadyCollectedSpecimen)
derivedUnitUuid
- propertyPaths
- java.util.List<Point> findPointsForFieldUnitList(java.util.List<java.util.UUID> fieldUnitUuids)
fieldUnitUuids
- FieldUnitDTO loadFieldUnitDTO(java.util.UUID derivedUnitUuid)
derivedUnitUuid
with all intermediate derivatives and GatheringEventDTO
derivedUnitUuid
- Copyright © 2007-2020 EDIT. All Rights Reserved.