public interface ITaxonDao extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase>, IPublishableDao<TaxonBase>
Modifier and Type | Method and Description |
---|---|
Taxon |
acceptedTaxonFor(Synonym synonym,
Classification classificationFilter,
java.util.List<java.lang.String> propertyPaths)
This method was originally required when synonyms still had a synonym relationship
to taxa and could belong to multiple taxa.
|
long |
count(java.lang.Class<? extends TaxonBase> type,
java.util.List<Restriction<?>> restrictions,
boolean includePublished) |
long |
countAcceptedTaxonFor(Synonym synonym,
Classification classificationFilter)
This method was originally required when synonyms still had a synonym relationship
to taxa and could belong to multiple taxa.
|
<S extends TaxonBase> |
countByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode)
Counts all taxa which match the given identifier (identifier type, identifier string and match mode).
|
<S extends TaxonBase> |
countByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter)
Counts all taxa which have the given marker of type markerType and with value markerValue.
|
long |
countMatchesByName(java.lang.String queryString,
MatchMode matchMode,
boolean onlyAcccepted) |
long |
countMatchesByName(java.lang.String queryString,
MatchMode matchMode,
boolean onlyAcccepted,
java.util.List<org.hibernate.criterion.Criterion> criteria) |
long |
countSynonyms(boolean onlyAttachedToTaxon)
Counts the number of synonyms
|
long |
countSynonyms(Synonym synonym,
SynonymType type)
Returns a count of the synonyms (where relationship.type == type,
if this argument is supplied) which do have an accepted taxon.
|
long |
countSynonyms(Taxon taxon,
SynonymType type)
Returns a count of the Synonyms (where relationship.type == type,
if this argument is supplied) where the supplied taxon is relatedTo.
|
long |
countTaxaByCommonName(java.lang.String searchString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
long |
countTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean doIncludeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished) |
long |
countTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank)
Returns a count of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
long |
countTaxonRelationships(java.util.Set<TaxonRelationshipType> types) |
long |
countTaxonRelationships(Taxon taxon,
java.util.Set<TaxonRelationshipType> types,
boolean includeUnpublished,
RelationshipBase.Direction direction) |
long |
countTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
RelationshipBase.Direction direction)
Returns a count of the TaxonRelationships (of where relationship.type ==
type, if this argument is supplied) where the supplied taxon either is
relatedFrom or relatedTo depending on the
direction
parameter. |
<S extends TaxonBase> |
findByIdentifier(java.lang.Class<S> clazz,
java.lang.String identifier,
DefinedTerm identifierType,
TaxonNode subtreeFilter,
MatchMode matchmode,
boolean includeEntity,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
<S extends TaxonBase> |
findByMarker(java.lang.Class<S> clazz,
MarkerType markerType,
java.lang.Boolean markerValue,
TaxonNode subtreeFilter,
boolean includeEntity,
TaxonTitleType titleType,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonBase> |
findByNameTitleCache(boolean doTaxa,
boolean doSynonyms,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order,
java.lang.Integer pageNumber,
java.lang.Integer pageSize,
java.util.List<java.lang.String> propertyPaths)
Find taxa by searching for Taxa and Synonyms where the
TaxonName .titleCache matches
the name specified as queryString taxonName |
TaxonBase |
findByUuid(java.util.UUID uuid,
java.util.List<org.hibernate.criterion.Criterion> criteria,
java.util.List<java.lang.String> propertyPaths)
Returns a taxon corresponding to the given uuid
|
java.util.List<? extends TaxonBase> |
findByUuids(java.util.List<java.util.UUID> uuids,
java.util.List<org.hibernate.criterion.Criterion> criteria,
java.util.List<java.lang.String> propertyPaths)
Returns a list of Taxon entities corresponding to the given uuid list.
|
java.util.Map<java.lang.String,java.util.Map<java.util.UUID,java.util.Set<TaxonName>>> |
findIdenticalNames(java.util.List<java.util.UUID> sourceRefUuids,
java.util.List<java.lang.String> propertyPaths)
see service layer documentation
|
java.util.List<TaxonBase> |
findTaxaByName(java.lang.Class<? extends TaxonBase> clazz,
java.lang.String uninomial,
java.lang.String infragenericEpithet,
java.lang.String specificEpithet,
java.lang.String infraspecificEpithet,
java.lang.String authorshipCache,
Rank rank,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances where the
taxon.name properties match the parameters passed.
|
java.util.List<Synonym> |
getSynonyms(Taxon taxon,
SynonymType type,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths)
Returns the Synonyms (of where relationship.type == type, if this argument is supplied)
that do have the supplied taxon as accepted taxon.
|
java.util.List<Taxon> |
getTaxaByCommonName(java.lang.String queryString,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<UuidAndTitleCache<Taxon>> |
getTaxaByCommonNameForEditor(java.lang.String titleSearchStringSqlized,
Classification classification,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas) |
java.util.List<TaxonBase> |
getTaxaByName(boolean doTaxa,
boolean doSynonyms,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeAuthors,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
boolean includeUnpublished,
NameSearchOrder order,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<java.lang.String> propertyPaths)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString.
|
java.util.List<TaxonBase> |
getTaxaByName(java.lang.String queryString,
java.lang.Boolean accepted,
boolean includeUnpublished,
Reference sec)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString, and taxon.sec matches the sec parameter.
|
java.util.List<TaxonBase> |
getTaxaByName(java.lang.String name,
boolean includeUnpublished,
Reference sec)
Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter,
and taxon.sec matches the sec parameter.
|
java.util.List<TaxonBase> |
getTaxaByName(java.lang.String queryString,
MatchMode matchMode,
java.lang.Boolean accepted,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber)
Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
where the taxonBase.name.nameCache property matches the String queryString.
|
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> |
getTaxaByNameForEditor(boolean doTaxa,
boolean doSynonyms,
boolean doNamesWithoutTaxa,
boolean doMisappliedNames,
boolean doCommonNames,
boolean includeUnpublished,
java.lang.String queryString,
Classification classification,
TaxonNode subtree,
MatchMode matchMode,
java.util.Set<NamedArea> namedAreas,
NameSearchOrder order) |
java.util.List<TaxonRelationship> |
getTaxonRelationships(java.util.Set<TaxonRelationshipType> types,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths) |
java.util.List<TaxonRelationship> |
getTaxonRelationships(Taxon taxon,
java.util.Set<TaxonRelationshipType> type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
RelationshipBase.Direction direction) |
java.util.List<TaxonRelationship> |
getTaxonRelationships(Taxon taxon,
TaxonRelationshipType type,
boolean includeUnpublished,
java.lang.Integer pageSize,
java.lang.Integer pageNumber,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
RelationshipBase.Direction direction)
Returns the TaxonRelationships (of where relationship.type == type, if
this argument is supplied) where the supplied taxon either is
relatedFrom or relatedTo depending on the
direction
parameter. |
<S extends TaxonBase> |
list(java.lang.Class<S> type,
java.util.List<Restriction<?>> restrictions,
java.lang.Integer limit,
java.lang.Integer start,
java.util.List<OrderHint> orderHints,
java.util.List<java.lang.String> propertyPaths,
boolean includePublished) |
TaxonBase |
load(java.util.UUID uuid,
java.util.List<java.lang.String> propertyPaths)
Finds the cdm entity specified by the
uuid parameter and
recursively initializes all bean properties given in the
propertyPaths parameter. |
java.util.List<java.lang.String> |
taxaByNameNotInDB(java.util.List<java.lang.String> taxonNames) |
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, loadList, lock, merge, merge, refresh, refresh, replace, save, saveAll, saveOrUpdate, saveOrUpdateAll, update
countByTitle, countByTitle, countByTitle, findByTitle, findByTitle, findByTitle
count, optimizeIndex, purgeIndex, rebuildIndex, search, suggestQuery
load
TaxonBase load(java.util.UUID uuid, java.util.List<java.lang.String> propertyPaths)
uuid
parameter and
recursively initializes all bean properties given in the
propertyPaths
parameter.
For detailed description and examples please refer to:
IBeanInitializer.initialize(Object, List)
NOTE: Also taxa with publish=false
are returned.
load
in interface ICdmEntityDao<TaxonBase>
propertyPaths
- properties to be initializedjava.util.List<TaxonBase> getTaxaByName(java.lang.String name, boolean includeUnpublished, Reference sec)
name
- sec
- java.util.List<TaxonBase> getTaxaByName(java.lang.String queryString, java.lang.Boolean accepted, boolean includeUnpublished, Reference sec)
name
- sec
- java.util.List<TaxonBase> getTaxaByName(java.lang.String queryString, MatchMode matchMode, java.lang.Boolean accepted, boolean includeUnpublished, java.lang.Integer pageSize, java.lang.Integer pageNumber)
queryString
- matchMode
- accepted
- pageSize
- pageNumber
- java.util.List<TaxonBase> getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames, boolean includeAuthors, java.lang.String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, java.util.Set<NamedArea> namedAreas, boolean includeUnpublished, NameSearchOrder order, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
doTaxa
- doSynonyms
- queryString
- classification
- TODOsubtree
- matchMode
- namedAreas
- TODOpageSize
- pageNumber
- propertyPaths
- TODOlong countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames, boolean doIncludeAuthors, java.lang.String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, java.util.Set<NamedArea> namedAreas, boolean includeUnpublished)
doTaxa
- doSynonyms
- queryString
- classification
- TODOsubtree
- matchMode
- namedAreas
- pageSize
- pageNumber
- propertyPaths
- long countTaxaByName(java.lang.Class<? extends TaxonBase> clazz, java.lang.String uninomial, java.lang.String infragenericEpithet, java.lang.String specificEpithet, java.lang.String infraspecificEpithet, java.lang.String authorshipCache, Rank rank)
doTaxa
- doSynonyms
- uninomial
- infragenericEpithet
- specificEpithet
- infraspecificEpithet
- rank
- authorshipCache
- java.util.List<TaxonBase> findTaxaByName(java.lang.Class<? extends TaxonBase> clazz, java.lang.String uninomial, java.lang.String infragenericEpithet, java.lang.String specificEpithet, java.lang.String infraspecificEpithet, java.lang.String authorshipCache, Rank rank, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
Compare with
#findByName(String, MatchMode, int, int, boolean)
which searches for TaxonName
.titleCache
doTaxa
- doSynonyms
- uninomial
- infragenericEpithet
- specificEpithet
- infraspecificEpithet
- rank
- authorshipCache
- pageSize
- The maximum number of taxa returned (can be null for all matching taxa)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)java.util.List<TaxonBase> findByNameTitleCache(boolean doTaxa, boolean doSynonyms, boolean includeUnpublished, java.lang.String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, java.util.Set<NamedArea> namedAreas, NameSearchOrder order, java.lang.Integer pageNumber, java.lang.Integer pageSize, java.util.List<java.lang.String> propertyPaths)
TaxonName
.titleCache
matches
the name specified as queryString taxonName
Compare with
#findTaxaByName(Class, String, String, String, String, Rank, Integer, Integer)
which searches for TaxonName
.nameCache
queryString
- the taqxon Name to search forclassification
- TODOmatchMode
- namedAreas
- TODOpageNumber
- pageSize
- onlyAcccepted
- TaxonBase findByUuid(java.util.UUID uuid, java.util.List<org.hibernate.criterion.Criterion> criteria, java.util.List<java.lang.String> propertyPaths)
uuid
- The uuid of the taxon requestedcriteria
- Custom criteria to be added to the default list of applied criteria.propertyPaths
- java.util.List<? extends TaxonBase> findByUuids(java.util.List<java.util.UUID> uuids, java.util.List<org.hibernate.criterion.Criterion> criteria, java.util.List<java.lang.String> propertyPaths)
uuids
- criteria
- propertyPaths
- java.util.List<Taxon> getTaxaByCommonName(java.lang.String queryString, Classification classification, MatchMode matchMode, java.util.Set<NamedArea> namedAreas, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
queryString
- classification
- matchMode
- namedAreas
- pageSize
- pageNumber
- propertyPaths
- long countSynonyms(boolean onlyAttachedToTaxon)
onlyAttachedToTaxon
- if true
only those synonyms being attached to
an accepted taxon are countedlong countMatchesByName(java.lang.String queryString, MatchMode matchMode, boolean onlyAcccepted)
queryString
- matchMode
- onlyAcccepted
- long countMatchesByName(java.lang.String queryString, MatchMode matchMode, boolean onlyAcccepted, java.util.List<org.hibernate.criterion.Criterion> criteria)
queryString
- matchMode
- onlyAcccepted
- criteria
- long countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, boolean includeUnpublished, RelationshipBase.Direction direction)
direction
parameter.taxon
- The taxon that is relatedFromtype
- The type of TaxonRelationship (can be null)direction
- specifies the direction of the relationshiplong countTaxonRelationships(Taxon taxon, java.util.Set<TaxonRelationshipType> types, boolean includeUnpublished, RelationshipBase.Direction direction)
java.util.List<TaxonRelationship> getTaxonRelationships(Taxon taxon, TaxonRelationshipType type, boolean includeUnpublished, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths, RelationshipBase.Direction direction)
direction
parameter.taxon
- The taxon that is relatedTotype
- The type of TaxonRelationship (can be null)pageSize
- The maximum number of relationships returned (can be null for
all relationships)pageNumber
- The offset (in pageSize chunks) from the start of the result
set (0 - based)orderHints
- Properties to order bypropertyPaths
- Properties to initialize in the returned entities, following
the syntax described in
IBeanInitializer.initialize(Object, List)
direction
- specifies the direction of the relationshipjava.util.List<TaxonRelationship> getTaxonRelationships(Taxon taxon, java.util.Set<TaxonRelationshipType> type, boolean includeUnpublished, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths, RelationshipBase.Direction direction)
long countSynonyms(Taxon taxon, SynonymType type)
taxon
- The taxon that is relatedTotype
- The type of Synonym (can be null)java.util.List<Synonym> getSynonyms(Taxon taxon, SynonymType type, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
taxon
- The accepted taxontype
- The type of synonym (can be null)pageSize
- The maximum number of synonyms returned (can be null for all synonyms)pageNumber
- The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param orderHints Properties to order bypropertyPaths
- Properties to initialize in the returned entities, following the syntax described in IBeanInitializer.initialize(Object, List)
List
of Synonym
instanceslong countSynonyms(Synonym synonym, SynonymType type)
synonym
- The synonym that is relatedFromtype
- The type of Synonym (can be null)long countTaxaByCommonName(java.lang.String searchString, Classification classification, MatchMode matchMode, java.util.Set<NamedArea> namedAreas)
java.util.Map<java.lang.String,java.util.Map<java.util.UUID,java.util.Set<TaxonName>>> findIdenticalNames(java.util.List<java.util.UUID> sourceRefUuids, java.util.List<java.lang.String> propertyPaths)
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doNamesWithoutTaxa, boolean doMisappliedNames, boolean doCommonNames, boolean includeUnpublished, java.lang.String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, java.util.Set<NamedArea> namedAreas, NameSearchOrder order)
java.util.List<java.lang.String> taxaByNameNotInDB(java.util.List<java.lang.String> taxonNames)
Taxon acceptedTaxonFor(Synonym synonym, Classification classificationFilter, java.util.List<java.lang.String> propertyPaths)
synonym
- classificationFilter
- propertyPaths
- countAcceptedTaxonFor(Synonym, Classification)
long countAcceptedTaxonFor(Synonym synonym, Classification classificationFilter)
classificationFilter
- #acceptedTaxonFor(Synonym, Classification, Integer, Integer, List, List)
java.util.List<UuidAndTitleCache<Taxon>> getTaxaByCommonNameForEditor(java.lang.String titleSearchStringSqlized, Classification classification, MatchMode matchMode, java.util.Set<NamedArea> namedAreas)
<S extends TaxonBase> java.util.List<java.lang.Object[]> findByIdentifier(java.lang.Class<S> clazz, java.lang.String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode, boolean includeEntity, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
<S extends TaxonBase> long countByIdentifier(java.lang.Class<S> clazz, java.lang.String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode)
clazz
- optional, the TaxonBase subclassidentifier
- the identifier stringidentifierType
- the identifier typematchmode
- the match mode for the identifier stringsubtreeFilter
- the subtree filter as taxon node<S extends TaxonBase> long countByMarker(java.lang.Class<S> clazz, MarkerType markerType, java.lang.Boolean markerValue, TaxonNode subtreeFilter)
clazz
- markerType
- markerValue
- subtreeFilter
- <S extends TaxonBase> java.util.List<java.lang.Object[]> findByMarker(java.lang.Class<S> clazz, MarkerType markerType, java.lang.Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity, TaxonTitleType titleType, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<java.lang.String> propertyPaths)
clazz
- markerType
- markerValue
- subtreeFilter
- includeEntity
- pageSize
- pageNumber
- propertyPaths
- long countTaxonRelationships(java.util.Set<TaxonRelationshipType> types)
types
- java.util.List<TaxonRelationship> getTaxonRelationships(java.util.Set<TaxonRelationshipType> types, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
types
- pageSize
- pageNumber
- orderHints
- propertyPaths
- <S extends TaxonBase> java.util.List<S> list(java.lang.Class<S> type, java.util.List<Restriction<?>> restrictions, java.lang.Integer limit, java.lang.Integer start, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths, boolean includePublished)
type
- restrictions
- limit
- start
- orderHints
- propertyPaths
- includePublished
- long count(java.lang.Class<? extends TaxonBase> type, java.util.List<Restriction<?>> restrictions, boolean includePublished)
type
- restrictions
- includePublished
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