eu.etaxonomy.cdm.persistence.dao.taxon
Interface ITaxonDao

All Superinterfaces:

IAnnotatableDao<TaxonBase>, ICdmEntityDao<TaxonBase>, IIdentifiableDao<TaxonBase>, ISearchableDao<TaxonBase>, ITitledDao<TaxonBase>, IVersionableDao<TaxonBase>

All Known Implementing Classes:

TaxonDaoHibernateImpl

public interface ITaxonDao
extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase>

Author:

a.mueller

Method Summary

int	countAllRelationships()
int	countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted)
int	countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<org.hibernate.criterion.Criterion> criteria)
Integer	countSynonymRelationships(TaxonBase taxonBase, SynonymRelationshipType type, RelationshipBase.Direction relatedfrom)
int	countSynonyms(Synonym synonym, SynonymRelationshipType type) Returns a count of the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied synonym is relatedFrom.
int	countSynonyms(Taxon taxon, SynonymRelationshipType type) Returns a count of the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo.
long	countTaxaByCommonName(String searchString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas)
long	countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas)
int	countTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank) Returns a count of TaxonBase instances where the taxon.name properties match the parameters passed.
int	countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, 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.
long	deleteSynonymRelationships(Synonym syn, Taxon taxon) Deletes all synonym relationships of a given synonym.
List<TaxonBase>	findByNameTitleCache(boolean doTaxa, boolean doSynonyms, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths) Find taxa by searching for Taxa and Synonyms where the TaxonNameBase.titleCache matches the name specified as queryString taxonName
TaxonBase	findByUuid(UUID uuid, List<org.hibernate.criterion.Criterion> criteria, List<String> propertyPaths) Returns a taxon corresponding to the given uuid
List<? extends TaxonBase>	findByUuids(List<UUID> uuids, List<org.hibernate.criterion.Criterion> criteria, List<String> propertyPaths) Returns a list of Taxon entities corresponding to the given uuid list.
List<TaxonNameBase>	findIdenticalNamesNew(List<String> propertyPaths)
List<UUID>	findIdenticalTaxonNameIds(List<String> propertyPath)
List<TaxonNameBase>	findIdenticalTaxonNames(List<String> propertyPath) Creates all inferred synonyms for the species in the tree and insert it to the database
List<TaxonBase>	findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber) Returns a list of TaxonBase instances where the taxon.name properties match the parameters passed.
List<RelationshipBase>	getAllRelationships(Integer limit, Integer start)
List<Synonym>	getAllSynonyms(Integer limit, Integer start)
List<Taxon>	getAllTaxa(Integer limit, Integer start)
List<TaxonBase>	getAllTaxonBases(Integer pagesize, Integer page) TODO necessary?
String	getPhylumName(TaxonNameBase name)
List<Taxon>	getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths) Deprecated. obsolete when using classification
List<Taxon>	getRootTaxa(Reference sec) Deprecated. obsolete when using classification
List<Taxon>	getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications) Deprecated. obsolete when using classification
List<SynonymRelationship>	getSynonymRelationships(TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths, RelationshipBase.Direction relatedfrom)
List<SynonymRelationship>	getSynonyms(Synonym synoynm, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied synonym is relatedFrom.
List<SynonymRelationship>	getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied taxon is relatedTo.
List<Object[]>	getTaxaByCommonName(String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, List<String> propertyPaths)
List<TaxonBase>	getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, List<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.
List<TaxonBase>	getTaxaByName(String queryString, Boolean accepted, 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.
List<TaxonBase>	getTaxaByName(String queryString, MatchMode matchMode, Boolean accepted, Integer pageSize, 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.
List<TaxonBase>	getTaxaByName(String name, Reference sec) Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter, and taxon.sec matches the sec parameter.
List<UuidAndTitleCache<TaxonBase>>	getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas)
List<UuidAndTitleCache<TaxonNode>>	getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification)
List<TaxonRelationship>	getTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<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.
List<UuidAndTitleCache<TaxonBase>>	getUuidAndTitleCacheSynonym()
List<UuidAndTitleCache<TaxonBase>>	getUuidAndTitleCacheTaxon()
List<String>	taxaByNameNotInDB(List<String> taxonNames)

Methods inherited from interface eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao

countByReferenceTitle, countByTitle, countRights, countSources, countTitleCache, find, findByReferenceTitle, findByTitle, findOriginalSourceByIdInSource, findTitleCache, getRights, getSources, getUuidAndTitleCache

Methods inherited from interface eu.etaxonomy.cdm.persistence.dao.common.IAnnotatableDao

countAnnotations, countMarkers, countMarkers, getAnnotations, getMarkers, groupMarkers

Methods inherited from interface eu.etaxonomy.cdm.persistence.dao.common.IVersionableDao

countAuditEvents, countAuditEvents, getAuditEvents, getAuditEvents, getNextAuditEvent, getPreviousAuditEvent

Methods inherited from interface eu.etaxonomy.cdm.persistence.dao.common.ICdmEntityDao

clear, count, count, count, delete, exists, findById, findByUuid, flush, getSession, getType, group, list, list, list, list, list, list, list, listByIds, load, load, load, lock, merge, refresh, refresh, replace, rows, save, saveAll, saveOrUpdate, saveOrUpdateAll, update

Methods inherited from interface eu.etaxonomy.cdm.persistence.dao.common.ITitledDao

countByTitle, countByTitle, countByTitle, findByTitle, findByTitle, findByTitle, findByTitleAndClass

Methods inherited from interface eu.etaxonomy.cdm.persistence.dao.common.ISearchableDao

count, optimizeIndex, purgeIndex, rebuildIndex, search, suggestQuery

Method Detail

getTaxaByName

List<TaxonBase> getTaxaByName(String name,
                              Reference sec)

Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter, and taxon.sec matches the sec parameter.

Parameters:

name -

sec -

Returns:

getTaxaByName

List<TaxonBase> getTaxaByName(String queryString,
                              Boolean accepted,
                              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.

Parameters:

name -

sec -

Returns:

getTaxaByName

List<TaxonBase> getTaxaByName(String queryString,
                              MatchMode matchMode,
                              Boolean accepted,
                              Integer pageSize,
                              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.

Parameters:

queryString -

matchMode -

accepted -

pageSize -

pageNumber -

Returns:

getTaxaByName

List<TaxonBase> getTaxaByName(boolean doTaxa,
                              boolean doSynonyms,
                              boolean doMisappliedNames,
                              String queryString,
                              Classification classification,
                              MatchMode matchMode,
                              Set<NamedArea> namedAreas,
                              Integer pageSize,
                              Integer pageNumber,
                              List<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.

Parameters:

doTaxa -

doSynonyms -

queryString -

classification - TODO

matchMode -

namedAreas - TODO

pageSize -

pageNumber -

propertyPaths - TODO

Returns:

list of found taxa

countTaxaByName

long countTaxaByName(boolean doTaxa,
                     boolean doSynonyms,
                     boolean doMisappliedNames,
                     String queryString,
                     Classification classification,
                     MatchMode matchMode,
                     Set<NamedArea> namedAreas)

Parameters:

doTaxa -

doSynonyms -

queryString -

classification - TODO

matchMode -

namedAreas -

pageSize -

pageNumber -

propertyPaths -

Returns:

countTaxaByName

int countTaxaByName(Class<? extends TaxonBase> clazz,
                    String uninomial,
                    String infragenericEpithet,
                    String specificEpithet,
                    String infraspecificEpithet,
                    Rank rank)

Returns a count of TaxonBase instances where the taxon.name properties match the parameters passed.

Parameters:

doTaxa -

doSynonyms -

uninomial -

infragenericEpithet -

specificEpithet -

infraspecificEpithet -

rank -

Returns:

a count of TaxonBase instances

findTaxaByName

List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz,
                               String uninomial,
                               String infragenericEpithet,
                               String specificEpithet,
                               String infraspecificEpithet,
                               Rank rank,
                               Integer pageSize,
                               Integer pageNumber)

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

Compare with #findByName(String, MatchMode, int, int, boolean) which searches for TaxonNameBase.titleCache

Parameters:

doTaxa -

doSynonyms -

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

findByNameTitleCache

List<TaxonBase> findByNameTitleCache(boolean doTaxa,
                                     boolean doSynonyms,
                                     String queryString,
                                     Classification classification,
                                     MatchMode matchMode,
                                     Set<NamedArea> namedAreas,
                                     Integer pageNumber,
                                     Integer pageSize,
                                     List<String> propertyPaths)

Find taxa by searching for Taxa and Synonyms where the TaxonNameBase.titleCache matches the name specified as queryString taxonName

Compare with findTaxaByName(Class, String, String, String, String, Rank, Integer, Integer) which searches for TaxonNameBase.nameCache

Parameters:

queryString - the taqxon Name to search for

classification - TODO

matchMode -

namedAreas - TODO

pageNumber -

pageSize -

onlyAcccepted -

Returns:

findByUuid

TaxonBase findByUuid(UUID uuid,
                     List<org.hibernate.criterion.Criterion> criteria,
                     List<String> propertyPaths)

Returns a taxon corresponding to the given uuid

Parameters:

uuid - The uuid of the taxon requested

criteria - Custom criteria to be added to the default list of applied criteria.

propertyPaths -

Returns:

findByUuids

List<? extends TaxonBase> findByUuids(List<UUID> uuids,
                                      List<org.hibernate.criterion.Criterion> criteria,
                                      List<String> propertyPaths)

Returns a list of Taxon entities corresponding to the given uuid list.

Parameters:

uuids -

criteria -

propertyPaths -

Returns:

getTaxaByCommonName

List<Object[]> getTaxaByCommonName(String queryString,
                                   Classification classification,
                                   MatchMode matchMode,
                                   Set<NamedArea> namedAreas,
                                   Integer pageSize,
                                   Integer pageNumber,
                                   List<String> propertyPaths)

Parameters:

queryString -

classification -

matchMode -

namedAreas -

pageSize -

pageNumber -

propertyPaths -

Returns:

A List of arrays. Each entry array holds the following entities: Taxon, CommonName, Description, Feature

getRootTaxa

List<Taxon> getRootTaxa(Reference sec)

Deprecated. obsolete when using classification

Computes all Taxon instances that do not have a taxonomic parent and has at least one child.

Returns:

The List of root taxa.

getRootTaxa

List<Taxon> getRootTaxa(Reference sec,
                        CdmFetch cdmFetch,
                        Boolean onlyWithChildren,
                        Boolean withMisapplications)

Deprecated. obsolete when using classification

Computes all Taxon instances that do not have a taxonomic parent.

Parameters:

sec - The concept reference that the taxon belongs to

cdmFetch - not used yet !! TODO

onlyWithChildren - if true only taxa are returned that have taxonomic children.
Default: true.

withMisaplications - if false only taxa are returned that have no isMisappliedNameFor relationship.
Default: true.

Returns:

The List of root taxa.

getRootTaxa

List<Taxon> getRootTaxa(Rank rank,
                        Reference sec,
                        CdmFetch cdmFetch,
                        Boolean onlyWithChildren,
                        Boolean withMisapplications,
                        List<String> propertyPaths)

Deprecated. obsolete when using classification

Computes all Taxon instances which name is of a certain Rank.

Parameters:

rank - The rank of the taxon name

sec - The concept reference that the taxon belongs to

cdmFetch - not used yet !! TODO

onlyWithChildren - if true only taxa are returned that have taxonomic children.
Default: true.

withMisaplications - if false only taxa are returned that have no isMisappliedNameFor relationship.

propertyPaths - properties to be initialized, For detailed description and examples please refer to: IBeanInitializer.initialize(Object, List).
Default: true.

Returns:

The List of root taxa.

getAllTaxonBases

List<TaxonBase> getAllTaxonBases(Integer pagesize,
                                 Integer page)

TODO necessary?

Parameters:

pagesize - max maximum number of returned taxa

page - page to start, with 0 being first page

Returns:

getAllTaxa

List<Taxon> getAllTaxa(Integer limit,
                       Integer start)

Parameters:

limit -

start -

Returns:

getAllSynonyms

List<Synonym> getAllSynonyms(Integer limit,
                             Integer start)

Parameters:

limit -

start -

Returns:

getAllRelationships

List<RelationshipBase> getAllRelationships(Integer limit,
                                           Integer start)

countAllRelationships

int countAllRelationships()

countMatchesByName

int countMatchesByName(String queryString,
                       MatchMode matchMode,
                       boolean onlyAcccepted)

Parameters:

queryString -

matchMode -

onlyAcccepted -

Returns:

countMatchesByName

int countMatchesByName(String queryString,
                       MatchMode matchMode,
                       boolean onlyAcccepted,
                       List<org.hibernate.criterion.Criterion> criteria)

Parameters:

queryString -

matchMode -

onlyAcccepted -

criteria -

Returns:

countTaxonRelationships

int countTaxonRelationships(Taxon taxon,
                            TaxonRelationshipType type,
                            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.

Parameters:

taxon - The taxon that is relatedFrom

type - The type of TaxonRelationship (can be null)

direction - specifies the direction of the relationship

Returns:

the number of TaxonRelationship instances

getTaxonRelationships

List<TaxonRelationship> getTaxonRelationships(Taxon taxon,
                                              TaxonRelationshipType type,
                                              Integer pageSize,
                                              Integer pageNumber,
                                              List<OrderHint> orderHints,
                                              List<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.

Parameters:

taxon - The taxon that is relatedTo

type - 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 by

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

direction - specifies the direction of the relationship

Returns:

a List of TaxonRelationship instances

countSynonyms

int countSynonyms(Taxon taxon,
                  SynonymRelationshipType type)

Returns a count of the SynonymRelationships (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 SynonymRelationship (can be null)

Returns:

the number of SynonymRelationship instances

getSynonyms

List<SynonymRelationship> getSynonyms(Taxon taxon,
                                      SynonymRelationshipType type,
                                      Integer pageSize,
                                      Integer pageNumber,
                                      List<OrderHint> orderHints,
                                      List<String> propertyPaths)

Returns the SynonymRelationships (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 SynonymRelationship (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) * @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 List of SynonymRelationship instances

countSynonyms

int countSynonyms(Synonym synonym,
                  SynonymRelationshipType type)

Returns a count of the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied synonym is relatedFrom.

Parameters:

taxon - The synonym that is relatedFrom

type - The type of SynonymRelationship (can be null)

Returns:

the number of SynonymRelationship instances

getSynonyms

List<SynonymRelationship> getSynonyms(Synonym synoynm,
                                      SynonymRelationshipType type,
                                      Integer pageSize,
                                      Integer pageNumber,
                                      List<OrderHint> orderHints,
                                      List<String> propertyPaths)

Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) where the supplied synonym is relatedFrom.

Parameters:

taxon - The synonym that is relatedFrom

type - The type of SynonymRelationship (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) * @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 List of SynonymRelationship instances

getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification

List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification)

Returns:

findIdenticalTaxonNames

List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath)

Creates all inferred synonyms for the species in the tree and insert it to the database

Parameters:

tree -

Returns:

List of inferred synonyms

getPhylumName

String getPhylumName(TaxonNameBase name)

countTaxaByCommonName

long countTaxaByCommonName(String searchString,
                           Classification classification,
                           MatchMode matchMode,
                           Set<NamedArea> namedAreas)

deleteSynonymRelationships

long deleteSynonymRelationships(Synonym syn,
                                Taxon taxon)

Deletes all synonym relationships of a given synonym. If taxon is given only those relationships to the taxon are deleted.

Parameters:

synonym - the synonym

taxon - the taxon, may be null

Returns:

findIdenticalTaxonNameIds

List<UUID> findIdenticalTaxonNameIds(List<String> propertyPath)

findIdenticalNamesNew

List<TaxonNameBase> findIdenticalNamesNew(List<String> propertyPaths)

countSynonymRelationships

Integer countSynonymRelationships(TaxonBase taxonBase,
                                  SynonymRelationshipType type,
                                  RelationshipBase.Direction relatedfrom)

getSynonymRelationships

List<SynonymRelationship> getSynonymRelationships(TaxonBase taxonBase,
                                                  SynonymRelationshipType type,
                                                  Integer pageSize,
                                                  Integer pageNumber,
                                                  List<OrderHint> orderHints,
                                                  List<String> propertyPaths,
                                                  RelationshipBase.Direction relatedfrom)

getUuidAndTitleCacheTaxon

List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon()

Returns:

getUuidAndTitleCacheSynonym

List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym()

Returns:

getTaxaByNameForEditor

List<UuidAndTitleCache<TaxonBase>> getTaxaByNameForEditor(boolean doTaxa,
                                                          boolean doSynonyms,
                                                          String queryString,
                                                          Classification classification,
                                                          MatchMode matchMode,
                                                          Set<NamedArea> namedAreas)

taxaByNameNotInDB

List<String> taxaByNameNotInDB(List<String> taxonNames)