public interface IOccurrenceDao extends IIdentifiableDao<SpecimenOrObservationBase>
Modifier and Type | Method and Description |
---|---|
long |
count(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
TaxonBase determinedAs)
Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase
|
long |
count(java.lang.Class<? extends SpecimenOrObservationBase> clazz,
TaxonName determinedAs)
Returns the number of occurences belonging to a certain subclass - which must extend SpecimenOrObservationBase
|
long |
countByGeneticAccessionNumber(java.lang.String accessionNumberString)
Returns count of derivedUnits that has a sequence with the accession number and is determined to a taxon
|
long |
countDerivationEvents(SpecimenOrObservationBase occurence)
Returns a count of derivation events that have involved creating new DerivedUnits from this occurence
|
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 |
countMedia(SpecimenOrObservationBase occurence)
Returns a count of Media that are associated with a given occurence
|
<T extends SpecimenOrObservationBase> |
countOccurrences(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType recordBasis,
Taxon associatedTaxon,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the number of specimens that match the given parameters
Note: Specifying a taxon will already check the name of this
taxon, its synonymy and the synonym names for determinations of the
specimen.
|
DnaSample |
findByGeneticAccessionNumber(java.lang.String accessionNumberString,
java.util.List<java.lang.String> propertyPaths)
Returns
DerivedUnit that has the accession number and is determined to a taxon |
java.util.List<FieldUnit> |
findFieldUnitsForGatheringEvent(java.util.UUID gatheringEventUuid,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns all
FieldUnit s that are referencing this GatheringEvent |
<T extends SpecimenOrObservationBase> |
findOccurrences(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType type,
Taxon determinedAs,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Queries the database for specimens which match the given criteria
Note: Specifying a taxon will already check the name of this taxon, its synonymy and the synonym names for determinations of the specimen. |
<T extends SpecimenOrObservationBase> |
findOccurrencesUuidAndTitleCache(java.lang.Class<T> clazz,
java.lang.String queryString,
java.lang.String significantIdentifier,
SpecimenOrObservationType type,
Taxon determinedAs,
TaxonName associatedTaxonName,
MatchMode matchmode,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints) |
java.util.List<SpecimenOrObservationBase> |
findOriginalsForDerivedUnit(java.util.UUID derivedUnitUuid,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<Point> |
findPointsForFieldUnitList(java.util.List<java.util.UUID> fieldUnitUuids) |
java.util.List<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
|
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. |
java.util.List<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 and for a given taxon concept
|
java.util.List<UuidAndTitleCache<FieldUnit>> |
getFieldUnitUuidAndTitleCache()
Retrieves the
UUID and the string representation (title cache) of all
FieldUnit s found in the data base. |
java.util.List<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
|
java.util.List<SpecimenOrObservationBase> |
list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonBase determinedAs,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of SpecimenOrObservationBase instances stored in the database.
|
java.util.List<SpecimenOrObservationBase> |
list(java.lang.Class<? extends SpecimenOrObservationBase> type,
TaxonName determinedAs,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns a sublist of SpecimenOrObservationBase instances stored in the database.
|
<T extends SpecimenOrObservationBase> |
listByAssociatedTaxon(java.lang.Class<T> type,
Taxon associatedTaxon,
java.lang.Integer limit,
java.lang.Integer start,
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. |
<T extends SpecimenOrObservationBase> |
listByAssociatedTaxonName(java.lang.Class<T> type,
TaxonName associatedTaxonName,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Lists all instances of
SpecimenOrObservationBase which are determined as the taxon name specified as parameter. |
java.util.Collection<SpecimenOrObservationBase> |
listBySpecimenOrObservationType(SpecimenOrObservationType type,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Retrieves all
SpecimenOrObservationBase s that have the given SpecimenOrObservationType . |
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<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<SpecimenTypeDesignation> |
listTypeDesignations(SpecimenOrObservationBase<?> 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. |
<T extends SpecimenOrObservationBase> |
listUuidAndTitleCacheByAssociatedTaxon(java.lang.Class<T> type,
Taxon associatedTaxon,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints) |
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 findOccurrences(Class, String, String, SpecimenOrObservationType, Taxon, TaxonName, MatchMode, Integer, Integer, List, List) |
countByIdentifier, countByMarker, countByReferenceTitle, countByReferenceTitleWithRestrictions, countByTitle, countByTitleWithRestrictions, countRights, countSources, countTitleCache, find, findByIdentifier, findByMarker, findByReferenceTitle, findByReferenceTitleWithRestrictions, findByTitle, findByTitleWithRestrictions, findOriginalSourceByIdInSource, findTitleCache, getRights, getSources, getTitleCache, getUuidAndTitleCache, getUuidAndTitleCache, getUuidAndTitleCache, getUuidAndTitleCacheByMarker
countAnnotations, countMarkers, countMarkers, getAnnotations, getMarkers, groupMarkers
countAuditEvents, countAuditEvents, getAuditEvents, getAuditEvents, getNextAuditEvent, getPreviousAuditEvent
clear, count, count, count, count, countByParam, countByParamWithRestrictions, delete, exists, findById, findByParam, findByParam, findByParamWithRestrictions, findByUuid, findByUuidWithoutFlush, flush, getSession, getType, group, list, list, list, list, list, list, list, list, list, load, load, load, loadList, lock, merge, merge, refresh, refresh, replace, save, saveAll, saveOrUpdate, saveOrUpdateAll, update
countByTitle, countByTitle, countByTitle, findByTitle, findByTitle, findByTitle
count, optimizeIndex, purgeIndex, rebuildIndex, search, suggestQuery
long count(java.lang.Class<? extends SpecimenOrObservationBase> clazz, TaxonName determinedAs)
clazz
- optionally restrict the counted occurrences to those of a certain subclass of SpecimenOrObservationBasedeterminedAs
- the taxon name that these specimens are determined to belong tojava.util.List<SpecimenOrObservationBase> list(java.lang.Class<? extends SpecimenOrObservationBase> type, TaxonName determinedAs, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
type
- determinedAs
- the taxon name that these specimens are determined to belong toorderHints
- Supports path like orderHints.propertyNames
which
include *-to-one properties like createdBy.username or
authorTeam.persistentTitleCacheorg.springframework.dao.DataAccessException
long count(java.lang.Class<? extends SpecimenOrObservationBase> clazz, TaxonBase determinedAs)
clazz
- optionally restrict the counted occurrences to those of a certain subclass of SpecimenOrObservationBasedeterminedAs
- the taxon concept that these specimens are determined to belong tojava.util.List<SpecimenOrObservationBase> list(java.lang.Class<? extends SpecimenOrObservationBase> type, TaxonBase determinedAs, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
type
- determinedAs
- the taxon concept that these specimens are determined to belong toorderHints
- Supports path like orderHints.propertyNames
which
include *-to-one properties like createdBy.username or
authorTeam.persistentTitleCacheorg.springframework.dao.DataAccessException
<T extends SpecimenOrObservationBase> java.util.List<T> findOccurrences(java.lang.Class<T> clazz, java.lang.String queryString, java.lang.String significantIdentifier, SpecimenOrObservationType type, Taxon determinedAs, TaxonName associatedTaxonName, MatchMode matchmode, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
clazz
- 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.associatedTaxonName
- the taxon name that the specimens have been determined asmatchmode
- 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.persistentTitleCachepropertyPaths
- <T extends SpecimenOrObservationBase> java.util.List<UuidAndTitleCache<SpecimenOrObservationBase>> findOccurrencesUuidAndTitleCache(java.lang.Class<T> clazz, java.lang.String queryString, java.lang.String significantIdentifier, SpecimenOrObservationType type, Taxon determinedAs, TaxonName associatedTaxonName, MatchMode matchmode, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints)
clazz
- queryString
- significantIdentifier
- type
- determinedAs
- associatedTaxonName
- matchmode
- limit
- start
- orderHints
- propertyPaths
- findOccurrences(Class, String, String, SpecimenOrObservationType, Taxon, TaxonName, MatchMode, Integer, Integer, List, List)
<T extends SpecimenOrObservationBase> long countOccurrences(java.lang.Class<T> clazz, java.lang.String queryString, java.lang.String significantIdentifier, SpecimenOrObservationType recordBasis, Taxon associatedTaxon, TaxonName associatedTaxonName, MatchMode matchmode, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
clazz
- 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.associatedTaxonName
- the taxon name that the specimens have been determined asmatchmode
- 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.persistentTitleCachelong countMedia(SpecimenOrObservationBase occurence)
occurence
- the occurence associated with these mediajava.util.List<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)
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)java.util.List<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)propertyPaths
- properties to initialize - see IBeanInitializer.initialize(Object, List)
long countDerivationEvents(SpecimenOrObservationBase occurence)
occurence
- the occurence that was a source of these derivation eventsjava.util.List<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)propertyPaths
- properties to initialize - see IBeanInitializer.initialize(Object, List)
java.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
<T extends SpecimenOrObservationBase> java.util.List<T> listByAssociatedTaxonName(java.lang.Class<T> type, TaxonName associatedTaxonName, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
SpecimenOrObservationBase
which are determined as the taxon name
specified as parameter.T
- type
- associatedTaxonName
- limit
- start
- orderHints
- propertyPaths
- <T extends SpecimenOrObservationBase> java.util.List<T> listByAssociatedTaxon(java.lang.Class<T> type, Taxon associatedTaxon, java.lang.Integer limit, java.lang.Integer start, 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
or a TaxonName
may be referenced by the DeterminationEvent
of the SpecimenOrObservationBase
T
- type
- associatedTaxon
- limit
- start
- orderHints
- propertyPaths
- <T extends SpecimenOrObservationBase> java.util.List<UuidAndTitleCache<SpecimenOrObservationBase>> listUuidAndTitleCacheByAssociatedTaxon(java.lang.Class<T> type, Taxon associatedTaxon, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints)
type
- associatedTaxon
- limit
- start
- orderHints
- propertyPaths
- listByAssociatedTaxon(Class, Taxon, Integer, Integer, List, List)
java.util.Collection<SpecimenNodeWrapper> listUuidAndTitleCacheByAssociatedTaxon(java.util.List<java.util.UUID> taxonNodeUuids, java.lang.Integer limit, java.lang.Integer start)
findOccurrences(Class, String, String, SpecimenOrObservationType, Taxon, TaxonName, MatchMode, Integer, Integer, List, List)
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<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<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<SpecimenTypeDesignation> listTypeDesignations(SpecimenOrObservationBase<?> 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<SpecimenOrObservationBase> listBySpecimenOrObservationType(SpecimenOrObservationType type, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
SpecimenOrObservationBase
s that have the given SpecimenOrObservationType
.type
- limit
- start
- orderHints
- propertyPaths
- java.util.List<FieldUnit> findFieldUnitsForGatheringEvent(java.util.UUID gatheringEventUuid, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
FieldUnit
s that are referencing this GatheringEvent
gatheringEventUuid
- the UUID
of the gathering eventlimit
- start
- orderHints
- propertyPaths
- long countByGeneticAccessionNumber(java.lang.String accessionNumberString)
accessionNumber
- propertyPaths
- DnaSample findByGeneticAccessionNumber(java.lang.String accessionNumberString, java.util.List<java.lang.String> propertyPaths)
DerivedUnit
that has the accession number and is determined to a taxonaccessionNumber
- propertyPaths
- java.util.List<SpecimenOrObservationBase> findOriginalsForDerivedUnit(java.util.UUID derivedUnitUuid, java.util.List<java.lang.String> propertyPaths)
derivedUnitUuid
- java.util.List<Point> findPointsForFieldUnitList(java.util.List<java.util.UUID> fieldUnitUuids)
fieldUnitUuids
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