eu.etaxonomy.cdm.api.service

Interface ITaxonService

All Superinterfaces:

IAnnotatableService<TaxonBase>, IIdentifiableEntityService<TaxonBase>, IPublishableService<TaxonBase>, IService<TaxonBase>, IVersionableService<TaxonBase>

All Known Implementing Classes:

TaxonServiceImpl

public interface ITaxonService
extends IIdentifiableEntityService<TaxonBase>, IPublishableService<TaxonBase>

Method Summary

Modifier and Type	Method and Description
void	changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon, boolean setBasionymRelationIfApplicable) Changes the homotypic group of a synonym into the new homotypic group.
UpdateResult	changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon, TaxonRelationshipType oldRelationshipType, SynonymType synonymType) Change a related concept into synonym
UpdateResult	changeRelatedTaxonToSynonym(java.util.UUID fromTaxonUuid, java.util.UUID toTaxonUuid, TaxonRelationshipType oldRelationshipType, SynonymType synonymType)
UpdateResult	changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym) Changes a synonym into an accepted taxon and removes the synonym relationship to the given accepted taxon.
UpdateResult	changeSynonymToAcceptedTaxon(java.util.UUID synonymUuid, java.util.UUID acceptedTaxonUuid, java.util.UUID newParentNodeUuid, boolean deleteSynonym)
UpdateResult	changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference reference, java.lang.String microReference) Change a synonym into a related concept
UpdateResult	changeSynonymToRelatedTaxon(java.util.UUID synonymUuid, java.util.UUID toTaxonUuid, TaxonRelationshipType taxonRelationshipType, Reference citation, java.lang.String microcitation)
long	countSynonyms(boolean onlyAttachedToTaxon) Counts the number of synonyms
java.util.List<Synonym>	createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames) Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database
java.util.List<Synonym>	createInferredSynonyms(Taxon taxon, Classification tree, SynonymType type, boolean doWithMisappliedNames) Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
DeleteResult	deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config) Removes a synonym. In detail it removes the synonym concept If removeNameIfPossible is true it also removes the synonym name if it is not used in any other context (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...) If newHomotypicGroupIfNeeded is true and the synonym name is not deleted and the name is homotypic to the taxon the name is moved to a new homotypic group. If synonym is null the method has no effect.
DeleteResult	deleteSynonym(java.util.UUID synonymUuid, SynonymDeletionConfigurator config) Removes a synonym.
DeleteResult	deleteTaxon(java.util.UUID taxonUuid, TaxonDeletionConfigurator config, java.util.UUID classificationUuid)
Taxon	findAcceptedTaxonFor(java.util.UUID synonymUuid, java.util.UUID classificationUuid, boolean includeUnpublished, java.util.List<java.lang.String> propertyPaths)
Synonym	findBestMatchingSynonym(java.lang.String taxonName, boolean includeUnpublished)
Taxon	findBestMatchingTaxon(MatchingTaxonConfigurator config)
Taxon	findBestMatchingTaxon(java.lang.String taxonName)
Pager<SearchResult<TaxonBase>>	findByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz, java.lang.String queryString, Classification classification, TaxonNode subtree, java.util.List<Feature> features, 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) Searches for TaxonBase instances by using the DescriptionElement free text index.
Pager<SearchResult<TaxonBase>>	findByDistribution(java.util.List<NamedArea> areaFilter, java.util.List<PresenceAbsenceTerm> statusFilter, Classification classification, TaxonNode subtree, java.lang.Integer pageSize, java.lang.Integer pageNumber, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths)
Pager<SearchResult<TaxonBase>>	findByEverythingFullText(java.lang.String queryString, Classification classification, TaxonNode subtree, boolean includeUnpublished, 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) Deprecated. this search should fully be covered by the new method #findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List) , maybe we should rename this latter method to give it a more meaningful name
Pager<SearchResult<TaxonBase>>	findByFullText(java.lang.Class<? extends TaxonBase> clazz, java.lang.String queryString, Classification classification, TaxonNode subtree, boolean includeUnpublished, 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) Searches for TaxonBase instances using the TaxonBase free text index.
<S extends TaxonBase> Pager<IdentifiedEntityDTO<S>>	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> Pager<MarkedEntityDTO<S>>	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) Returns a pager for DTOs that hold the marker including type, title and uuid and the according TaxonBase information (uuid, title and the taxon object itself (optional)).
java.util.Map<java.lang.String,java.util.Map<java.util.UUID,java.util.Set<TaxonName>>>	findIdenticalTaxonNames(java.util.List<java.util.UUID> sourceRefUuids, java.util.List<java.lang.String> propertyPaths) Returns a map of taxon names that have identical name caches but derive from different sources.
Pager<IdentifiableEntity>	findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator) Returns a list of IdentifiableEntity instances (in particular, TaxonName and TaxonBase instances) that match the properties specified in the configurator.
Pager<SearchResult<TaxonBase>>	findTaxaAndNamesByFullText(java.util.EnumSet<TaxaAndNamesSearchMode> searchModes, java.lang.String queryString, Classification classification, TaxonNode subtree, java.util.Set<NamedArea> namedAreas, java.util.Set<PresenceAbsenceTerm> distributionStatus, 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) Searches for TaxonBase instances using the TaxonBase free text index.
java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>>	findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator)
java.util.List<TaxonBase>	findTaxaByID(java.util.Set<java.lang.Integer> listOfIDs)
Pager<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<TaxonBase>	findTaxaByName(MatchingTaxonConfigurator config)
TaxonBase	findTaxonByUuid(java.util.UUID uuid, java.util.List<java.lang.String> propertyPaths) Returns the TaxonBase with the given UUID using the given match mode and initialization strategy
java.util.List<java.util.List<Synonym>>	getHeterotypicSynonymyGroups(Taxon taxon, java.util.List<java.lang.String> propertyPaths) Returns the ordered list of all homotypical groups that contain synonyms that are heterotypic to the given taxon.
java.util.List<Synonym>	getHomotypicSynonymsByHomotypicGroup(Taxon taxon, java.util.List<java.lang.String> propertyPaths) Returns the list of all synonyms that share the same homotypical group with the given taxon.
Pager<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 (with the given synonym relationship type, if this argument is supplied) that do have the supplied taxon as accepted taxon.
java.util.List<java.util.List<Synonym>>	getSynonymsByHomotypicGroup(Taxon taxon, java.util.List<java.lang.String> propertyPaths) This method returns in the first entry the list of synonyms of the homotypic group of the accepted taxon.
java.util.List<Classification>	listClassifications(TaxonBase taxonBase, java.lang.Integer limit, java.lang.Integer start, java.util.List<java.lang.String> propertyPaths) Lists all classifications the given taxon/synonym is used inSynonym
java.util.List<TaxonRelationship>	listFromTaxonRelationships(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) Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedFrom.
IncludedTaxaDTO	listIncludedTaxa(java.util.UUID taxonUuid, IncludedTaxonConfiguration configuration) Returns all taxa which are congruent or included in the taxon represented by the given taxon uuid.
java.util.List<Media>	listMedia(Taxon taxon, java.util.Set<TaxonRelationshipEdge> includeRelationships, java.lang.Boolean limitToGalleries, java.lang.Boolean includeTaxonDescriptions, java.lang.Boolean includeOccurrences, java.lang.Boolean includeTaxonNameDescriptions, java.util.List<java.lang.String> propertyPath) Lists all Media found in an any TaxonDescription, NameDescription, SpecimenOrObservationBase, DnaSample Chromatograms, etc.
java.util.Set<Taxon>	listRelatedTaxa(Taxon taxon, java.util.Set<TaxonRelationshipEdge> includeRelationships, java.lang.Integer maxDepth, boolean includeUnpublished, java.lang.Integer limit, java.lang.Integer start, java.util.List<java.lang.String> propertyPaths) lists all taxa which are related to the taxon given as parameter.
java.util.List<TaxonBase>	listTaxaByName(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<Media>	listTaxonDescriptionMedia(Taxon taxon, java.util.Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, java.util.List<java.lang.String> propertyPath) Deprecated. use #listMedia(Taxon, Set, boolean, boolean, List) instead
java.util.List<TaxonRelationship>	listTaxonRelationships(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) Returns all or a page of all taxon concept relationships in the database.
TaxonRelationshipsDTO	listTaxonRelationships(java.util.UUID taxonUuid, java.util.Set<TaxonRelationshipType> directTypes, java.util.Set<TaxonRelationshipType> inversTypes, RelationshipBase.Direction direction, boolean groupMisapplications, boolean includeUnpublished, java.lang.Integer pageSize, java.lang.Integer pageNumber) Returns a list of taxon relationships for a given taxon as DTO.
java.util.List<TaxonRelationship>	listToTaxonRelationships(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) Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedTo.
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.
UpdateResult	moveFactualDateToAnotherTaxon(java.util.UUID fromTaxonUuid, java.util.UUID toTaxonUuid)
UpdateResult	moveSynonymToAnotherTaxon(Synonym oldSynonym, Taxon newTaxon, boolean moveHomotypicGroup, SynonymType newSynonymType) See moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)
UpdateResult	moveSynonymToAnotherTaxon(Synonym oldSynonym, Taxon newTaxon, boolean moveHomotypicGroup, SynonymType newSynonymType, Reference newSecundum, java.lang.String newSecundumDetail, boolean keepSecundumIfUndefined) Moves a synonym to another taxon and removes the old synonym relationship.
UpdateResult	moveSynonymToAnotherTaxon(Synonym oldSynonym, java.util.UUID newTaxonUUID, boolean moveHomotypicGroup, SynonymType newSynonymType, Reference newSecundum, java.lang.String newSecundumDetail, boolean keepSecundumIfUndefined)
<S extends TaxonBase> Pager<S>	page(java.lang.Class<S> clazz, java.util.List<Restriction<?>> restrictions, java.lang.Integer pageSize, java.lang.Integer pageIndex, java.util.List<OrderHint> orderHints, java.util.List<java.lang.String> propertyPaths, boolean includeUnpublished)
Pager<TaxonRelationship>	pageFromTaxonRelationships(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) Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedFrom.
Pager<TaxonRelationship>	pageToTaxonRelationships(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) Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo.
Pager<TaxonBase>	search(java.lang.Class<? extends TaxonBase> clazz, java.lang.String queryString, 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 TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
java.util.List<TaxonBase>	searchByName(java.lang.String name, boolean includeUnpublished, Reference sec) Returns a list of taxa that matches the name string and the sec reference
UpdateResult	swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean setNameInSource) Swaps given synonym and accepted taxon.
UpdateResult	swapSynonymAndAcceptedTaxon(java.util.UUID synonymUUid, java.util.UUID acceptedTaxonUuid, boolean setNameInSource)

Methods inherited from interface eu.etaxonomy.cdm.api.service.IIdentifiableEntityService

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

Methods inherited from interface eu.etaxonomy.cdm.api.service.IAnnotatableService

countMarkers, getAnnotations, getMarkers, groupMarkers

Methods inherited from interface eu.etaxonomy.cdm.api.service.IVersionableService

getNextAuditEvent, getPreviousAuditEvent, isDeletable, pageAuditEvents, pageAuditEvents

Methods inherited from interface eu.etaxonomy.cdm.api.service.IService

clear, count, delete, delete, delete, exists, find, find, find, find, findById, findWithoutFlush, getSession, group, list, list, load, load, load, loadByIds, loadByIds, loadWithUpdate, lock, merge, merge, merge, merge, page, page, page, pageByParamWithRestrictions, refresh, refresh, save, save, saveOrUpdate, saveOrUpdate, update

Methods inherited from interface eu.etaxonomy.cdm.api.service.IPublishableService

load

Method Detail

load

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.

For detailed description and examples please refer to: IBeanInitializer.initialize(Object, List)

NOTE: Also taxa with publish=false are returned.

Specified by:

load in interface IService<TaxonBase>

Returns:

the cdm entity or null if not object with given uuid exists or uuid is null

searchByName

java.util.List<TaxonBase> searchByName(java.lang.String name,
                                       boolean includeUnpublished,
                                       Reference sec)

Returns a list of taxa that matches the name string and the sec reference

Parameters:

name - the name string to search for

sec - the taxons sec reference

Returns:

a list of taxa matching the name and the sec reference

swapSynonymAndAcceptedTaxon

UpdateResult swapSynonymAndAcceptedTaxon(Synonym synonym,
                                         Taxon acceptedTaxon,
                                         boolean setNameInSource)

Swaps given synonym and accepted taxon. In particular:

• A new accepted taxon with the synonyms name is created
• The synonym is deleted from the old accepted taxons synonym list
• A new synonym with the name of the old accepted taxon is created
• The newly created synonym get related to the newly created accepted taxon

Parameters:

synonym -

acceptedTaxon -

setNameInSource -

Returns:

changeSynonymToAcceptedTaxon

UpdateResult changeSynonymToAcceptedTaxon(Synonym synonym,
                                          Taxon acceptedTaxon,
                                          boolean deleteSynonym)
                                   throws HomotypicalGroupChangeException

Changes a synonym into an accepted taxon and removes the synonym relationship to the given accepted taxon. Other synonyms homotypic to the synonym to change are moved to the same new accepted taxon as homotypic synonyms. The new accepted taxon has the same name and the same sec reference as the old synonym.
If the given accepted taxon and the synonym are homotypic to each other an exception may be thrown as taxonomically it doesn't make sense to have two accepted taxa in the same homotypic group but also it is than difficult to decide how to handle other names in the homotypic group. It is up to the implementing class to handle this situation via an exception or in another way.

Parameters:

synonym - the synonym to change into an accepted taxon

acceptedTaxon - an accepted taxon, the synonym had a relationship to

deleteSynonym - if true the method tries to delete the old synonym from the database

Returns:

the newly created accepted taxon

Throws:

java.lang.IllegalArgumentException - if the given accepted taxon and the synonym are homotypic to each other an exception may be thrown as taxonomically it doesn't make sense to have two accepted taxa in the same homotypic group but also it is than difficult to decide how to handle other names in the homotypic group. It is up to the implementing class to handle this situation via an exception or in another way.

HomotypicalGroupChangeException

changeSynonymToAcceptedTaxon

UpdateResult changeSynonymToAcceptedTaxon(java.util.UUID synonymUuid,
                                          java.util.UUID acceptedTaxonUuid,
                                          java.util.UUID newParentNodeUuid,
                                          boolean deleteSynonym)
                                   throws HomotypicalGroupChangeException

Parameters:

synonymUuid -

acceptedTaxonUuid -

newParentNodeUuid -

deleteSynonym -

Returns:

Throws:

HomotypicalGroupChangeException

changeSynonymToRelatedTaxon

UpdateResult changeSynonymToRelatedTaxon(Synonym synonym,
                                         Taxon toTaxon,
                                         TaxonRelationshipType taxonRelationshipType,
                                         Reference reference,
                                         java.lang.String microReference)

Change a synonym into a related concept

Parameters:

synonym - the synonym to change into the concept taxon

toTaxon - the taxon the newly created concept should be related to

taxonRelationshipType - the type of relationship

reference -

microReference -

Returns:

update result with the newly created concept

changeRelatedTaxonToSynonym

UpdateResult changeRelatedTaxonToSynonym(Taxon fromTaxon,
                                         Taxon toTaxon,
                                         TaxonRelationshipType oldRelationshipType,
                                         SynonymType synonymType)
                                  throws DataChangeNoRollbackException

Change a related concept into synonym

Parameters:

synonym - the concept taxon to change into a synonym

toTaxon - the taxon the newly created synonym should be related to

oldRelationshipType - the type of old concept relationship

synonymRelationshipType - the type of new synonym relationship

Returns:

update result with the newly created synonym

Throws:

DataChangeNoRollbackException

changeHomotypicalGroupOfSynonym

void changeHomotypicalGroupOfSynonym(Synonym synonym,
                                     HomotypicalGroup newHomotypicalGroup,
                                     Taxon targetTaxon,
                                     boolean setBasionymRelationIfApplicable)

Changes the homotypic group of a synonym into the new homotypic group. All relations to taxa are updated correctly depending on the homotypic group of the accepted taxon.
All existing basionym relationships to and from this name are removed.
If the parameter targetTaxon is defined, the synonym is added to this taxon irrespctive of if it has been related to this taxon before.
If setBasionymRelationIfApplicable is true a basionym relationship between the existing basionym(s) of the new homotypic group and the synonyms name is added.

Parameters:

synonym -

newHomotypicalGroup -

taxon -

setBasionymRelationIfApplicable -

moveSynonymToAnotherTaxon

UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym,
                                       Taxon newTaxon,
                                       boolean moveHomotypicGroup,
                                       SynonymType newSynonymType)
                                throws HomotypicalGroupChangeException

See moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)

Parameters:

oldSynonym -

newTaxon -

moveHomotypicGroup -

newSynonymType -

Returns:

Throws:

HomotypicalGroupChangeException

moveSynonymToAnotherTaxon

UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym,
                                       Taxon newTaxon,
                                       boolean moveHomotypicGroup,
                                       SynonymType newSynonymType,
                                       Reference newSecundum,
                                       java.lang.String newSecundumDetail,
                                       boolean keepSecundumIfUndefined)
                                throws HomotypicalGroupChangeException

Moves a synonym to another taxon and removes the old synonym relationship.

Parameters:

oldSynonym - the old synonym to move.

newTaxon - the taxon the synonym will be moved to

moveHomotypicGroup - if the synonym belongs to a homotypic group with other synonyms and moveHomotypicGroup is true all these synonyms are moved to the new taxon, if false a HomotypicalGroupChangeException is thrown. moveHomotypicGroup has no effect if the synonym is the only synonym in it's homotypic group.

newSynonymType - the synonym type of the new synonyms. Default is heterotypic.

newSecundum - The secundum for the new synonyms).

newSecundumDetail - The secundum micro reference for the new synonym(s).

keepSecundumIfUndefined - if no newSecundum and/or no newSecundumDetail is defined they are taken from the old synonym(s) if keepSecundumIfUndefined is true. If false the secundum and the secundum detail will be taken only from the newSecundum and newSecundumDetail even if they are undefined (null).

Returns:

The new synonym relationship. If moveHomotypicGroup is true additionally created new synonym relationships must be retrieved separately from the new taxon.

Throws:

HomotypicalGroupChangeException - Exception is thrown if (1) synonym is homotypic to the old accepted taxon or (2) synonym is in homotypic group with other synonyms and moveHomotypicGroup is false

moveSynonymToAnotherTaxon

UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym,
                                       java.util.UUID newTaxonUUID,
                                       boolean moveHomotypicGroup,
                                       SynonymType newSynonymType,
                                       Reference newSecundum,
                                       java.lang.String newSecundumDetail,
                                       boolean keepSecundumIfUndefined)
                                throws HomotypicalGroupChangeException

Parameters:

oldSynonym -

newTaxonUUID -

moveHomotypicGroup -

newSynonymType -

reference -

referenceDetail -

keepReference -

Returns:

Throws:

HomotypicalGroupChangeException

See Also:

#moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)}

listToTaxonRelationships

java.util.List<TaxonRelationship> listToTaxonRelationships(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)

Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedTo.

Parameters:

taxon - The taxon that is relatedTo

type - The type of TaxonRelationship (can be null)

includeUnpublished - should unpublished related taxa also be returned?

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 by

propertyPaths - Properties to initialize in the returned entities, following the syntax described in IBeanInitializer.initialize(Object, List)

Returns:

a List of TaxonRelationship instances

pageToTaxonRelationships

Pager<TaxonRelationship> pageToTaxonRelationships(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)

Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo.

Parameters:

taxon - The taxon that is relatedTo

type - The type of TaxonRelationship (can be null)

includeUnpublished - should unpublished related taxa also be returned?

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 by

propertyPaths - Properties to initialize in the returned entities, following the syntax described in IBeanInitializer.initialize(Object, List)

Returns:

a Pager of TaxonRelationship instances

listFromTaxonRelationships

java.util.List<TaxonRelationship> listFromTaxonRelationships(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)

Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedFrom.

Parameters:

taxon - The taxon that is relatedFrom

type - The type of TaxonRelationship (can be null)

includeUnpublished - should unpublished related taxa also be returned?

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 by

propertyPaths - Properties to initialize in the returned entities, following the syntax described in IBeanInitializer.initialize(Object, List)

Returns:

a List of TaxonRelationship instances

pageFromTaxonRelationships

Pager<TaxonRelationship> pageFromTaxonRelationships(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)

Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied) where the supplied taxon is relatedFrom.

Parameters:

taxon - The taxon that is relatedFrom

type - The type of TaxonRelationship (can be null)

includeUnpublished - should unpublished related taxa also be returned?

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 by

propertyPaths - Properties to initialize in the returned entities, following the syntax described in IBeanInitializer.initialize(Object, List)

Returns:

a Pager of TaxonRelationship instances

listRelatedTaxa

java.util.Set<Taxon> listRelatedTaxa(Taxon taxon,
                                     java.util.Set<TaxonRelationshipEdge> includeRelationships,
                                     java.lang.Integer maxDepth,
                                     boolean includeUnpublished,
                                     java.lang.Integer limit,
                                     java.lang.Integer start,
                                     java.util.List<java.lang.String> propertyPaths)

lists all taxa which are related to the taxon given as parameter.

Parameters:

taxon -

includeRelationships -

maxDepth - 1 for one level, null for infinite depth, 0 will completely omit collecting related taxa.

limit -

start -

propertyPaths -

Returns:

listTaxonRelationships

java.util.List<TaxonRelationship> listTaxonRelationships(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)

Returns all or a page of all taxon concept relationships in the database. The result can be filtered by relationship types.

Parameters:

types - The taxon relationship type filter, if null no filter is set, if empty the result will also be empty

pageSize - the page size

pageStart - the number of the page

orderHints - the order hints

propertyPaths - the property path to initialize the resulting objects

Returns:

list of taxon relationships matching the filter criteria

listClassifications

java.util.List<Classification> listClassifications(TaxonBase taxonBase,
                                                   java.lang.Integer limit,
                                                   java.lang.Integer start,
                                                   java.util.List<java.lang.String> propertyPaths)

Lists all classifications the given taxon/synonym is used inSynonym

Parameters:

taxonBase -

limit -

start -

propertyPaths -

Returns:

getSynonyms

Pager<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 (with the given synonym relationship type, if this argument is supplied) that do have the supplied taxon as accepted taxon.

Parameters:

taxon - The accepted taxon

type - The type of Synonym (can be null)

pageSize - The maximum number of synonyms returned (can be null for returning synonyms)

pageNumber - The offset (in pageSize chunks) from the start of the result set (0 - based) * @param orderHints Properties to order by

propertyPaths - Properties to initialize in the returned entities, following the syntax described in IBeanInitializer.initialize(Object, List)

Returns:

a Pager of Synonym instances

getSynonymsByHomotypicGroup

java.util.List<java.util.List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon,
                                                                    java.util.List<java.lang.String> propertyPaths)

This method returns in the first entry the list of synonyms of the homotypic group of the accepted taxon. All other entries represent the lists of heterotypic synonym groups. For detailed information about these 2 groups see getHomotypicSynonymsByHomotypicGroup(Taxon, List) and getHeterotypicSynonymyGroups(Taxon, List)

Parameters:

taxon - the accepted taxon

propertyPaths - the property path

Returns:

the list of groups of synonyms

See Also:

#getSynonyms(), SynonymType.HETEROTYPIC_SYNONYM_OF(), HomotypicalGroup

getHomotypicSynonymsByHomotypicGroup

java.util.List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon,
                                                             java.util.List<java.lang.String> propertyPaths)

Returns the list of all synonyms that share the same homotypical group with the given taxon. Only those homotypic synonyms are returned that do have a synonym relationship with the accepted taxon.

Parameters:

taxon -

propertyPaths -

Returns:

getHeterotypicSynonymyGroups

java.util.List<java.util.List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon,
                                                                     java.util.List<java.lang.String> propertyPaths)

Returns the ordered list of all homotypical groups that contain synonyms that are heterotypic to the given taxon. Taxon names of heterotypic synonyms belong to a homotypical group which cannot be the homotypical group to which the taxon name of the given taxon belongs. This method does not return the homotypic group the given taxon belongs to.
This method does neglect the type of synonym relationship that is defined between the given taxon and the synonym. So the synonym relationship may be homotypic however a synonym is returned in one of the result lists as long as the synonym does not belong to the same homotypic group as the given taxon.
The list returned is ordered according to the date of publication of the first published name within each homotypical group.

Parameters:

taxon -

propertyPaths -

Returns:

See Also:

#getHeterotypicSynonymyGroups(), #getSynonyms(), SynonymType.HETEROTYPIC_SYNONYM_OF(), HomotypicalGroup

search

Pager<TaxonBase> search(java.lang.Class<? extends TaxonBase> clazz,
                        java.lang.String queryString,
                        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 TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)

Specified by:

search in interface IIdentifiableEntityService<TaxonBase>

Parameters:

clazz - filter the results by class (or pass null to return all TaxonBase instances)

queryString -

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)

orderHints - Supports path like orderHints.propertyNames which include *-to-one properties like createdBy.username or authorTeam.persistentTitleCache

propertyPaths - properties to be initialized

Returns:

a Pager Taxon instances

See Also:

Apache Lucene - Query Parser Syntax

findTaxaByName

Pager<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. In order to search for any string value, pass '*', passing the string value of null will search for those taxa with a value of null in that field

Parameters:

clazz - optionally filter by class (can be null to return all taxa)

uninomial -

infragenericEpithet -

specificEpithet -

infraspecificEpithet -

rank -

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)

Returns:

a list of TaxonBase instances

listTaxaByName

java.util.List<TaxonBase> listTaxaByName(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. In order to search for any string value, pass '*', passing the string value of null will search for those taxa with a value of null in that field

Parameters:

clazz - optionally filter by class

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)

Returns:

a List of TaxonBase instances

findTaxaAndNames

Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator)

Returns a list of IdentifiableEntity instances (in particular, TaxonName and TaxonBase instances) that match the properties specified in the configurator.

Parameters:

configurator -

Returns:

findByEverythingFullText

@Deprecated
Pager<SearchResult<TaxonBase>> findByEverythingFullText(java.lang.String queryString,
                                                                    Classification classification,
                                                                    TaxonNode subtree,
                                                                    boolean includeUnpublished,
                                                                    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,
                                                                    LuceneMultiSearchException

Deprecated. this search should fully be covered by the new method #findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List) , maybe we should rename this latter method to give it a more meaningful name

performes a union searches for TaxonBase instances on all available free text indexes. At the time of writing this documentation it combines #findByDescriptionElementFullText(Class, String, Classification, List, List, boolean, Integer, Integer, List, List) and {@link #findByFullText(Class, String, Classification, List, boolean, Integer, Integer, List, List)

Parameters:

queryString - the query string

classification - Additional filter criterion: If a taxonomic classification three is specified here the result set will only contain taxa of the given classification

languages - Additional filter criterion: Search only in these languages. Not all text fields in the cdm model are multilingual, thus this setting will only apply to the multilingiual fields. Other fields are searched nevertheless if this parameter is set or not.

highlightFragments - TODO

pageSize - The maximum number of objects returned (can be null for all objects)

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.persistentTitleCache

propertyPaths - properties to initialize - see IBeanInitializer.initialize(Object, List)

Returns:

a paged list of instances of type T matching the queryString and the additional filter criteria

Throws:

LuceneCorruptIndexException

java.io.IOException

LuceneParseException

LuceneMultiSearchException

findByFullText

Pager<SearchResult<TaxonBase>> findByFullText(java.lang.Class<? extends TaxonBase> clazz,
                                              java.lang.String queryString,
                                              Classification classification,
                                              TaxonNode subtree,
                                              boolean includeUnpublished,
                                              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

Searches for TaxonBase instances using the TaxonBase free text index.

This is an experimental feature, it may be moved, modified, or even removed in future releases!!!

Parameters:

clazz - Additional filter criterion: The specific TaxonBase subclass to search for

queryString - the query string

classification - Additional filter criterion: If a taxonomic classification three is specified here the result set will only contain taxa of the given classification

languages - Additional filter criterion: Search only in these languages. Not all text fields in the cdm model are multilingual, thus this setting will only apply to the multilingiual fields. Other fields are searched nevertheless if this parameter is set or not.

highlightFragments - TODO

pageSize - The maximum number of objects returned (can be null for all objects)

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.persistentTitleCache

propertyPaths - properties to initialize - see IBeanInitializer.initialize(Object, List)

Returns:

a paged list of instances of type T matching the queryString and the additional filter criteria

Throws:

LuceneCorruptIndexException

java.io.IOException

LuceneParseException

findByDistribution

Pager<SearchResult<TaxonBase>> findByDistribution(java.util.List<NamedArea> areaFilter,
                                                  java.util.List<PresenceAbsenceTerm> statusFilter,
                                                  Classification classification,
                                                  TaxonNode subtree,
                                                  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

Parameters:

areaFilter -

statusFilter -

classification - Additional filter criterion: If a taxonomic classification three is specified here the result set will only contain taxa of the given classification

highlightFragments -

pageSize - The maximum number of objects returned (can be null for all objects)

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.persistentTitleCache

propertyPath - Common properties to initialize the instances of the CDM types (Taxon and Synonym this method can return - see IBeanInitializer.initialize(Object, List)

Returns:

a paged list of instances of Taxon instances

Throws:

java.io.IOException

LuceneParseException

findTaxaAndNamesByFullText

Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(java.util.EnumSet<TaxaAndNamesSearchMode> searchModes,
                                                          java.lang.String queryString,
                                                          Classification classification,
                                                          TaxonNode subtree,
                                                          java.util.Set<NamedArea> namedAreas,
                                                          java.util.Set<PresenceAbsenceTerm> distributionStatus,
                                                          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,
                                                          LuceneMultiSearchException

Searches for TaxonBase instances using the TaxonBase free text index.

This is an experimental feature, it may be moved, modified, or even removed in future releases!!!

Parameters:

searchModes - Additional filter criterion: defaults to [doTaxa] if set null

queryString - the query string

classification - Additional filter criterion: If a taxonomic classification three is specified here the result set will only contain taxa of the given classification

subtree -

namedAreas -

distributionStatus -

languages - Additional filter criterion: Search only in these languages. Not all text fields in the cdm model are multilingual, thus this setting will only apply to the multilingiual fields. Other fields are searched nevertheless if this parameter is set or not.

highlightFragments - TODO

pageSize - The maximum number of objects returned (can be null for all objects)

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.persistentTitleCache

propertyPath - Common properties to initialize the instances of the CDM types (Taxon and Synonym this method can return - see IBeanInitializer.initialize(Object, List)

Returns:

a paged list of instances of Taxon, Synonym, matching the queryString and the additional filter criteria

Throws:

LuceneCorruptIndexException

java.io.IOException

LuceneParseException

LuceneMultiSearchException

findByDescriptionElementFullText

Pager<SearchResult<TaxonBase>> findByDescriptionElementFullText(java.lang.Class<? extends DescriptionElementBase> clazz,
                                                                java.lang.String queryString,
                                                                Classification classification,
                                                                TaxonNode subtree,
                                                                java.util.List<Feature> features,
                                                                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

Searches for TaxonBase instances by using the DescriptionElement free text index.

This is an experimental feature, it may be moved, modified, or even removed in future releases!!!

Parameters:

clazz - Additional filter criterion:

queryString - the query string to filter by

classification - Additional filter criterion: If a taxonomic classification tree is specified here the result set will only contain taxa of the given classification

subtree - Additional filter criterion: If a taxonomic classification subtree is specified here the result set will only contain taxa of the given subtree

features - TODO

languages - Additional filter criterion: Search only in these languages. Not all text fields in the CDM model are multi-lingual, thus this setting will only apply to the multi-lingual fields. Other fields are searched nevertheless if this parameter is set or not.

highlightFragments - TODO

pageSize - The maximum number of objects returned (can be null for all objects)

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.persistentTitleCache

propertyPaths - properties to initialize - see IBeanInitializer.initialize(Object, List)

Returns:

a paged list of instances of type T matching the queryString and the additional filter criteria

Throws:

java.io.IOException

LuceneCorruptIndexException

LuceneParseException

listTaxonDescriptionMedia

@Deprecated
java.util.List<Media> listTaxonDescriptionMedia(Taxon taxon,
                                                            java.util.Set<TaxonRelationshipEdge> includeRelationships,
                                                            boolean limitToGalleries,
                                                            java.util.List<java.lang.String> propertyPath)

Deprecated. use #listMedia(Taxon, Set, boolean, boolean, List) instead

Lists all Media found in an any TaxonDescription associated with this taxon.

Parameters:

taxon -

includeRelationships - the given list of TaxonRelationshipEdges will be taken into account when retrieving media associated with the given taxon. Can be NULL.

limitToGalleries - whether to take only TaxonDescription into account which are marked as gallery

Returns:

listMedia

java.util.List<Media> listMedia(Taxon taxon,
                                java.util.Set<TaxonRelationshipEdge> includeRelationships,
                                java.lang.Boolean limitToGalleries,
                                java.lang.Boolean includeTaxonDescriptions,
                                java.lang.Boolean includeOccurrences,
                                java.lang.Boolean includeTaxonNameDescriptions,
                                java.util.List<java.lang.String> propertyPath)

Lists all Media found in an any TaxonDescription, NameDescription, SpecimenOrObservationBase, DnaSample Chromatograms, etc. associated with this taxon.

Parameters:

taxon -

includeRelationships - the given list of TaxonRelationshipEdges will be taken into account when retrieving media associated with the given taxon. Can be NULL.

limitToGalleries - whether to take only descriptions into account which are marked as gallery, can be NULL

includeTaxonDescriptions - whether to take TaxonDescriptions into account, can be NULL

includeOccurrences - whether to take TaxonDescriptions into account, can be NULL

includeTaxonNameDescriptions - whether to take TaxonNameDescriptions into account, can be NULL

propertyPath -

Returns:

findTaxaByID

java.util.List<TaxonBase> findTaxaByID(java.util.Set<java.lang.Integer> listOfIDs)

findTaxonByUuid

TaxonBase findTaxonByUuid(java.util.UUID uuid,
                          java.util.List<java.lang.String> propertyPaths)

Returns the TaxonBase with the given UUID using the given match mode and initialization strategy

Parameters:

uuid -

propertyPaths -

Returns:

countSynonyms

long countSynonyms(boolean onlyAttachedToTaxon)

Counts the number of synonyms

Parameters:

onlyAttachedToTaxon - if true only those synonyms being attached to an accepted taxon are counted

Returns:

the number of synonyms

findIdenticalTaxonNames

java.util.Map<java.lang.String,java.util.Map<java.util.UUID,java.util.Set<TaxonName>>> findIdenticalTaxonNames(java.util.List<java.util.UUID> sourceRefUuids,
                                                                                                               java.util.List<java.lang.String> propertyPaths)

Returns a map of taxon names that have identical name caches but derive from different sources. The sources are defined via the sources reference uuid.

Returns:

map of nameCaches and taxon name maps where the key is the UUID of the according sourceRefUuid

listIncludedTaxa

IncludedTaxaDTO listIncludedTaxa(java.util.UUID taxonUuid,
                                 IncludedTaxonConfiguration configuration)

Returns all taxa which are congruent or included in the taxon represented by the given taxon uuid. The result also returns the path to these taxa represented by the uuids of the taxon relationships types and doubtful information. If classificationUuids is set only taxa of classifications are returned which are included in the given classifications. ALso the path to these taxa may not include taxa from other classifications.

Parameters:

taxonUuid - uuid of the original taxon

classificationUuids - List of uuids of classifications used as a filter

includeDoubtful - set to true if also doubtfully included taxa should be included in the result

Returns:

a DTO which includes a list of taxa with the pathes from the original taxon to the given taxon as well as doubtful and date information. The original taxon is included in the result.

deleteSynonym

DeleteResult deleteSynonym(Synonym synonym,
                           SynonymDeletionConfigurator config)

Removes a synonym.

In detail it removes

the synonym concept

If removeNameIfPossible is true it also removes the synonym name if it is not used in any other context (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)

If newHomotypicGroupIfNeeded is true and the synonym name is not deleted and the name is homotypic to the taxon the name is moved to a new homotypic group.

If synonym is null the method has no effect.

Parameters:

taxon -

synonym -

removeNameIfPossible -

Returns:

deleteResult

deleteSynonym

DeleteResult deleteSynonym(java.util.UUID synonymUuid,
                           SynonymDeletionConfigurator config)

Removes a synonym. The method essentially loads the synonym and calls the deleteSynonym method

Parameters:

synonymUuid -

config -

Returns:

findBestMatchingTaxon

Taxon findBestMatchingTaxon(java.lang.String taxonName)

Parameters:

tnb -

Returns:

findBestMatchingTaxon

Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config)

findBestMatchingSynonym

Synonym findBestMatchingSynonym(java.lang.String taxonName,
                                boolean includeUnpublished)

findTaxaAndNamesForEditor

java.util.List<UuidAndTitleCache<? extends IdentifiableEntity>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator)

createInferredSynonyms

java.util.List<Synonym> createInferredSynonyms(Taxon taxon,
                                               Classification tree,
                                               SynonymType type,
                                               boolean doWithMisappliedNames)

Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database

Parameters:

taxon -

tree -

Returns:

list of inferred synonyms

createAllInferredSynonyms

java.util.List<Synonym> createAllInferredSynonyms(Taxon taxon,
                                                  Classification tree,
                                                  boolean doWithMisappliedNames)

Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database

Parameters:

taxon -

tree -

iDatabase -

Returns:

list of inferred synonyms

findAcceptedTaxonFor

Taxon findAcceptedTaxonFor(java.util.UUID synonymUuid,
                           java.util.UUID classificationUuid,
                           boolean includeUnpublished,
                           java.util.List<java.lang.String> propertyPaths)
                    throws UnpublishedException

Throws:

UnpublishedException

findTaxaByName

java.util.List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config)

findByIdentifier

<S extends TaxonBase> Pager<IdentifiedEntityDTO<S>> 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)

Parameters:

clazz - the optional TaxonBase subclass

identifier - the identifier string

identifierType - the identifier type

subtreeFilter - filter on a classification subtree (TaxonNode)

matchmode - the match mode for the identifier string

includeEntity - should the taxon as an object be included in the result

pageSize - page size

pageNumber - page number

propertyPaths - property path for initializing the returned taxon object (requires includeEntity=true)

Returns:

the resulting IdentifiedEntityDTO pager

See Also:

IIdentifiableEntityService.findByIdentifier(Class, String, DefinedTerm, MatchMode, boolean, Integer, Integer, List)

findByMarker

<S extends TaxonBase> Pager<MarkedEntityDTO<S>> 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)

Returns a pager for DTOs that hold the marker including type, title and uuid and the according TaxonBase information (uuid, title and the taxon object itself (optional)).

Parameters:

clazz - The optional TaxonBase subclass

markerType - the obligatory marker type, if not given, the results will always be empty

markerValue - the optional

subtreeFilter - filter on a classification subtree (TaxonNode)

includeEntity - should the taxon as an object be included in the result

titleType - which label to give the returned entity, taxon.titleCache, name.titleCache or name.nameCache

pageSize - page size

pageNumber - page number

propertyPaths - property path for initializing the returned taxon object (requires includeEntity=true)

Returns:

the resulting MarkedEntityDTO pager

See Also:

IIdentifiableEntityService.findByMarker(Class, MarkerType, Boolean, boolean, Integer, Integer, List)

swapSynonymAndAcceptedTaxon

UpdateResult swapSynonymAndAcceptedTaxon(java.util.UUID synonymUUid,
                                         java.util.UUID acceptedTaxonUuid,
                                         boolean setNameInSource)

Parameters:

synonymUUid -

acceptedTaxonUuid -

setNameInSource -

Returns:

deleteTaxon

DeleteResult deleteTaxon(java.util.UUID taxonUuid,
                         TaxonDeletionConfigurator config,
                         java.util.UUID classificationUuid)

Parameters:

taxonUuid -

config -

classificationUuid -

Returns:

moveFactualDateToAnotherTaxon

UpdateResult moveFactualDateToAnotherTaxon(java.util.UUID fromTaxonUuid,
                                           java.util.UUID toTaxonUuid)

changeSynonymToRelatedTaxon

UpdateResult changeSynonymToRelatedTaxon(java.util.UUID synonymUuid,
                                         java.util.UUID toTaxonUuid,
                                         TaxonRelationshipType taxonRelationshipType,
                                         Reference citation,
                                         java.lang.String microcitation)

Parameters:

synonymUuid -

toTaxonUuid -

taxonRelationshipType -

citation -

microcitation -

Returns:

changeRelatedTaxonToSynonym

UpdateResult changeRelatedTaxonToSynonym(java.util.UUID fromTaxonUuid,
                                         java.util.UUID toTaxonUuid,
                                         TaxonRelationshipType oldRelationshipType,
                                         SynonymType synonymType)
                                  throws DataChangeNoRollbackException

Parameters:

fromTaxonUuid -

toTaxonUuid -

oldRelationshipType -

synonymType -

Returns:

Throws:

DataChangeNoRollbackException

listTaxonRelationships

TaxonRelationshipsDTO listTaxonRelationships(java.util.UUID taxonUuid,
                                             java.util.Set<TaxonRelationshipType> directTypes,
                                             java.util.Set<TaxonRelationshipType> inversTypes,
                                             RelationshipBase.Direction direction,
                                             boolean groupMisapplications,
                                             boolean includeUnpublished,
                                             java.lang.Integer pageSize,
                                             java.lang.Integer pageNumber)

Returns a list of taxon relationships for a given taxon as DTO.

Parameters:

taxonUuid -

directTypes -

inversTypes -

direction -

groupMisapplications -

includeUnpublished -

pageSize -

pageNumber -

Returns:

page

<S extends TaxonBase> Pager<S> page(java.lang.Class<S> clazz,
                                    java.util.List<Restriction<?>> restrictions,
                                    java.lang.Integer pageSize,
                                    java.lang.Integer pageIndex,
                                    java.util.List<OrderHint> orderHints,
                                    java.util.List<java.lang.String> propertyPaths,
                                    boolean includeUnpublished)

Parameters:

clazz -

restrictions -

pageSize -

pageIndex -

orderHints -

propertyPaths -

includeUnpublished -

Returns: