package eu.etaxonomy.cdm.api.service;
import java.io.IOException;
+import java.util.EnumSet;
import java.util.List;
import java.util.Set;
import java.util.UUID;
import org.apache.lucene.queryParser.ParseException;
import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
+import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration;
import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
+import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
+import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO;
import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;
import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
-import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;
import eu.etaxonomy.cdm.api.service.search.SearchResult;
+import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.common.Language;
import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
import eu.etaxonomy.cdm.model.description.Feature;
+import eu.etaxonomy.cdm.model.description.PresenceAbsenceTermBase;
+import eu.etaxonomy.cdm.model.location.NamedArea;
import eu.etaxonomy.cdm.model.media.Media;
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
-import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
+import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
- /**
- * Computes all taxon bases.
- * @param limit
- * @param start
- * @return
- *
- * FIXME could substitute with list(Synonym.class, limit, start)
- */
- public List<Synonym> getAllSynonyms(int limit, int start);
-
- /**
- * Computes all taxon bases.
- * @param limit
- * @param start
- * @return
- *
- * FIXME could substitute with list(Taxon.class, limit,start)
- */
- public List<Taxon> getAllTaxa(int limit, int start);
-
/**
* Computes all Taxon instances that do not have a taxonomic parent.
* @param sec The concept reference that the taxon belongs to
* @return The List<Taxon> of root taxa.
* @deprecated obsolete when using classification
*/
+ @Deprecated
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren);
/**
* @param propertyPaths
* properties to be initialized, For detailed description and
* examples <b>please refer to:</b>
- * {@link BeanInitializer#initialize(Object, List)}. <Br>
+ * {@link IBeanInitializer#initialize(Object, List)}. <Br>
* Default: true.
* @return The List<Taxon> of root taxa.
* @deprecated obsolete when using classification
*/
+ @Deprecated
public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
/**
* @return
* @deprecated use TermService#getVocabulary(VocabularyType) instead
*/
+ @Deprecated
public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
/**
* 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.
- * TODO Open issue: does the old synonym need to be deleted from the database?
+ *
*
* @param synonym
* the synonym to change into an accepted taxon
public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference reference, String microReference);
/**
- * Deletes all synonym relationships of a given synonym. If taxon is given only those relationships to the taxon are deleted.
- * @param syn the synonym
+ * TODO still needed and correct?
+ * Change a synonym into a related concept
+ *
+ * @param synonym
+ * the synonym to change into the concept taxon
+ * @param toTaxon
+ * the taxon the newly created concept should be related to
+ * @param taxonRelationshipType
+ * the type of relationship
+ * @param reference
+ * @param microReference
+ * @return
+ * the newly created concept
+ * @throws DataChangeNoRollbackException
+ */
+ public Synonym changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon,
+ TaxonRelationshipType oldRelationshipType,
+ SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException;
+ /**
+ * Deletes all synonym relationships of a given synonym. If taxon is given
+ * only those relationships to the taxon are deleted.
+ *
+ * @param syn
+ * the synonym
* @param taxon
* @return
+ * @deprecated This method must no longer being used since the
+ * SynonymRelationship is annotated at the {@link Taxon} and at
+ * the {@link Synonym} with <code>orphanDelete=true</code>. Just
+ * remove the from and to entities from the relationship and
+ * hibernate will care for the deletion. Using this method can cause
+ * <code>StaleStateException</code> (see http://dev.e-taxonomy.eu/trac/ticket/3797)
+ *
*/
+ @Deprecated
public long deleteSynonymRelationships(Synonym syn, Taxon taxon);
/**
* Deletes a taxon from the underlying database according to the given {@link TaxonDeletionConfigurator configurator}.
* @param taxon
* @param config
- * @throws ReferencedObjectUndeletableException
+ *
*/
- public void deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config) throws ReferencedObjectUndeletableException;
+ public DeleteResult deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config, Classification classification) ;
/**
* Changes the homotypic group of a synonym into the new homotypic group.
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @return a List of TaxonRelationship instances
*/
public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @return a Pager of TaxonRelationship instances
*/
public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @return a List of TaxonRelationship instances
*/
public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @return a Pager of TaxonRelationship instances
*/
public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
+ /**
+ * lists all taxa which are related to the <code>taxon</code> given as
+ * parameter.
+ *
+ * @param taxon
+ * @param includeRelationships
+ * @param maxDepth
+ * <code>1</code> for one level, <code>null</code> for infinite
+ * depth, <code>0</code> will completely omit collecting related taxa.
+ * @param limit
+ * @param start
+ * @param propertyPaths
+ * @return
+ */
+ public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,
+ Integer limit, Integer start, List<String> propertyPaths);
+
+ /**
+ * lists all accepted taxa for the given {@link Synonym}
+ *
+ * @param taxonBase
+ * @param limit
+ * @param start
+ * @param propertyPaths
+ * @return
+ */
+ public List<Classification> listClassifications(TaxonBase taxonBase, Integer limit, Integer start, List<String> propertyPaths);
+
/**
* Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
* where the supplied synonym is relatedFrom.
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* * @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @return a Pager of SynonymRelationship instances
*/
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* * @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @return a Pager of SynonymRelationship instances
*/
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<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
+ * {@link #getHomotypicSynonymsByHomotypicGroup(Taxon, List)} and
+ * {@link #getHeterotypicSynonymyGroups(Taxon, List)}
+ *
+ * @see #getSynonyms()
+ * @see SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF()
+ * @see eu.etaxonomy.cdm.model.name.HomotypicalGroup
+
+ * @param taxon the accepted taxon
+ * @param propertyPaths the property path
+ * @return the list of groups of synonyms
+ */
+ public List<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<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.
* @return a Pager Taxon instances
* @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
*/
+ @Override
public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
/**
public Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator);
/**
+ * performes a union searches for TaxonBase instances on all available
+ * free text indexes. At the time of writing this documentation it combines
+ * {@link #findByDescriptionElementFullText(Class, String, Classification, List, List, boolean, Integer, Integer, List, List)}
+ * and {@link #findByFullText(Class, String, Classification, List, boolean, Integer, Integer, List, List)
+ *
+ * @param queryString
+ * the query string
+ * @param classification
+ * Additional filter criterion: If a taxonomic classification
+ * three is specified here the result set will only contain taxa
+ * of the given classification
+ * @param 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.
+ * @param highlightFragments
+ * TODO
+ * @param pageSize
+ * The maximum number of objects returned (can be null for all
+ * objects)
+ * @param pageNumber
+ * The offset (in pageSize chunks) from the start of the result
+ * set (0 - based)
+ * @param orderHints
+ * Supports path like <code>orderHints.propertyNames</code> which
+ * include *-to-one properties like createdBy.username or
+ * authorTeam.persistentTitleCache
+ * @param propertyPaths
+ * properties to initialize - see
+ * {@link IBeanInitializer#initialize(Object, List)}
+ * @return a paged list of instances of type T matching the queryString and
+ * the additional filter criteria
+ * @return
+ * @throws CorruptIndexException
+ * @throws IOException
+ * @throws ParseException
+ * @throws LuceneMultiSearchException
+ * @deprecated this search should fully be covered by the new method
+ * {@link #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
+ */
+ @Deprecated
+ public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,
+ Classification classification, List<Language> languages, boolean highlightFragments,
+ Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException;
+
+ /**
+ * Searches for TaxonBase instances using the TaxonBase free text index.
+ *
+ * <h4>This is an experimental feature, it may be moved, modified, or even
+ * removed in future releases!!!</h4>
+ *
+ * @param clazz
+ * Additional filter criterion: The specific TaxonBase subclass
+ * to search for
+ * @param queryString
+ * the query string
+ * @param classification
+ * Additional filter criterion: If a taxonomic classification
+ * three is specified here the result set will only contain taxa
+ * of the given classification
+ * @param 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.
+ * @param highlightFragments
+ * TODO
+ * @param pageSize
+ * The maximum number of objects returned (can be null for all
+ * objects)
+ * @param pageNumber
+ * The offset (in pageSize chunks) from the start of the result
+ * set (0 - based)
+ * @param orderHints
+ * Supports path like <code>orderHints.propertyNames</code> which
+ * include *-to-one properties like createdBy.username or
+ * authorTeam.persistentTitleCache
+ * @param propertyPaths
+ * properties to initialize - see
+ * {@link IBeanInitializer#initialize(Object, List)}
+ * @return a paged list of instances of type T matching the queryString and
+ * the additional filter criteria
+ * @throws CorruptIndexException
+ * @throws IOException
+ * @throws ParseException
+ */
+ public Pager<SearchResult<TaxonBase>> findByFullText(Class<? extends TaxonBase> clazz, String queryString, Classification classification,
+ List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
+ List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException;
+
+
+ /**
+ * @param areaFilter
+ * @param statusFilter
+ * @param classification
+ * Additional filter criterion: If a taxonomic classification
+ * three is specified here the result set will only contain taxa
+ * of the given classification
+ * @param highlightFragments
+ * @param pageSize
+ * The maximum number of objects returned (can be null for all
+ * objects)
+ * @param pageNumber
+ * The offset (in pageSize chunks) from the start of the result
+ * set (0 - based)
+ * @param orderHints
+ * Supports path like <code>orderHints.propertyNames</code> which
+ * include *-to-one properties like createdBy.username or
+ * authorTeam.persistentTitleCache
+ * @param propertyPath
+ * Common properties to initialize the instances of the
+ * CDM types ({@link Taxon} and {@link Synonym}
+ * this method can return - see {@link IBeanInitializer#initialize(Object, List)}
+ * @return a paged list of instances of {@link Taxon} instances
+ * @throws IOException
+ * @throws ParseException
+ */
+ public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTermBase<?>> statusFilter,
+ Classification classification,
+ Integer pageSize, Integer pageNumber,
+ List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, ParseException;
+
+ /**
+ * Searches for TaxonBase instances using the TaxonBase free text index.
+ *
+ *
+ *
+ * <h4>This is an experimental feature, it may be moved, modified, or even
+ * removed in future releases!!!</h4>
+ * @param searchModes
+ * Additional filter criterion: defaults to [doTaxa] if set null
+ * @param queryString
+ * the query string
+ * @param classification
+ * Additional filter criterion: If a taxonomic classification
+ * three is specified here the result set will only contain taxa
+ * of the given classification
+ * @param namedAreas
+ * @param 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.
+ * @param highlightFragments
+ * TODO
+ * @param pageSize
+ * The maximum number of objects returned (can be null for all
+ * objects)
+ * @param pageNumber
+ * The offset (in pageSize chunks) from the start of the result
+ * set (0 - based)
+ * @param orderHints
+ * Supports path like <code>orderHints.propertyNames</code> which
+ * include *-to-one properties like createdBy.username or
+ * authorTeam.persistentTitleCache
+ * @param propertyPath
+ * Common properties to initialize the instances of the
+ * CDM types ({@link Taxon} and {@link Synonym}
+ * this method can return - see {@link IBeanInitializer#initialize(Object, List)}
+ * @return a paged list of instances of {@link Taxon}, {@link Synonym}, matching the queryString and
+ * the additional filter criteria
+ * @throws CorruptIndexException
+ * @throws IOException
+ * @throws ParseException
+ * @throws LuceneMultiSearchException
+ */
+ public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(
+ EnumSet<TaxaAndNamesSearchMode> searchModes,
+ String queryString, Classification classification, Set<NamedArea> namedAreas, Set<PresenceAbsenceTermBase<?>> distributionStatus,
+ List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
+ List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException;
+
+ /**
+ * Searches for TaxonBase instances by using the DescriptionElement free text index.
+ *
* <h4>This is an experimental feature, it may be moved, modified, or even
* removed in future releases!!!</h4>
*
* @param clazz
+ * Additional filter criterion:
* @param queryString
* the query string to filter by
* @param classification
- * If a taxonomic classification three is specified here the
- * result set will only contain taxa of the given classification
- * @param features TODO
+ * Additional filter criterion: If a taxonomic classification
+ * three is specified here the result set will only contain taxa
+ * of the given classification
+ * @param features
+ * TODO
* @param languages
- * 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.
- * @param highlightFragments TODO
+ * 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.
+ * @param highlightFragments
+ * TODO
* @param pageSize
* The maximum number of objects returned (can be null for all
* objects)
* authorTeam.persistentTitleCache
* @param propertyPaths
* properties to initialize - see
- * {@link BeanInitializer#initialize(Object, List)}
- * @return a paged list of instances of type T matching the queryString
+ * {@link IBeanInitializer#initialize(Object, List)}
+ * @return a paged list of instances of type T matching the queryString and
+ * the additional filter criteria
* @throws IOException
* @throws CorruptIndexException
* @throws ParseException
* @param mimeTypes
* @return
*
- * FIXME candidate for harmonization - rename to listMedia()
+ * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
*/
+ @Deprecated
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
/**
- * Lists all Media found in an any TaxonDescription associated with this taxon.
+ * Lists all Media found in an any TaxonDescription associated with this
+ * taxon.
+ *
* @param taxon
- * @param limitToGalleries whether to take only TaxonDescription into account which are marked as gallery
+ * @param includeRelationships
+ * the given list of TaxonRelationshipEdges will be taken into
+ * account when retrieving media associated with the given taxon.
+ * Can be NULL.
+ * @param limitToGalleries
+ * whether to take only TaxonDescription into account which are
+ * marked as gallery
* @return
+ * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
*/
- public List<Media> listTaxonDescriptionMedia(Taxon taxon, boolean limitToGalleries, List<String> propertyPath);
+ @Deprecated
+ public List<Media> listTaxonDescriptionMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, List<String> propertyPath);
+ /**
+ * Lists all Media found in an any TaxonDescription, NameDescription,
+ * SpecimenOrObservationBase, DnaSample Chromatograms, etc. associated with this taxon.
+ *
+ * @param taxon
+ * @param includeRelationships
+ * the given list of TaxonRelationshipEdges will be taken into
+ * account when retrieving media associated with the given taxon.
+ * Can be NULL.
+ * @param limitToGalleries
+ * whether to take only descriptions into account which are
+ * marked as gallery, can be NULL
+ * @param includeTaxonDescriptions
+ * whether to take TaxonDescriptions into account, can be NULL
+ * @param includeOccurrences
+ * whether to take TaxonDescriptions into account, can be NULL
+ * @param includeTaxonNameDescriptions
+ * whether to take TaxonNameDescriptions into account, can be NULL
+ * @param propertyPath
+ * @return
+ */
+ public List<Media> listMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
+ Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,
+ Boolean includeTaxonNameDescriptions, List<String> propertyPath);
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
public int countAllRelationships();
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
+
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath);
+
public String getPhylumName(TaxonNameBase name);
public long deleteSynonymRelationships(Synonym syn);
-
/**
+ * Returns all {@link Taxon taxa} which are {@link TaxonRelationshipType#CONGRUENT_TO() congruent} or
+ * {@link TaxonRelationshipType#INCLUDES() 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 {@link TaxonRelationshipType taxon relationships types} and doubtful information.
+ * If classificationUuids is set only taxa of classifications are returned which are included
+ * in the given {@link Classification classifications}. ALso the path to these taxa may not include
+ * taxa from other classifications.
+ * @param taxonUuid uuid of the original taxon
+ * @param classificationUuids List of uuids of classifications used as a filter
+ * @param includeDoubtful set to <code>true</code> if also doubtfully included taxa should be included in the result
+ * @return 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.
+ */
+ public IncludedTaxaDTO listIncludedTaxa(UUID taxonUuid, IncludedTaxonConfiguration configuration);
+
+
+ /**
* Removes a synonym.<BR><BR>
*
* In detail it removes
* @param taxon
* @param synonym
* @param removeNameIfPossible
- * @throws DataChangeNoRollbackException
+ * @return deleteResult
+ *
*/
- public void deleteSynonym(Synonym synonym, Taxon taxon, boolean removeNameIfPossible, boolean newHomotypicGroupIfNeeded);
+ public DeleteResult deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config);
/**
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param orderHints Properties to order by
- * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
+ * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
* @param direction The direction of the relationship
* @return a List of SynonymRelationship instances
*/
*/
public List<Synonym> createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames);
- public Pager<SearchResult<TaxonBase>> findByFullText(Class<? extends TaxonBase> clazz, String queryString, Classification classification,
- List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
- List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException;
- public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,
- Classification classification, List<Language> languages, boolean highlightFragments,
- Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException;
+
+
+ /**
+ * Removes a synonym.<BR><BR>
+ *
+ * In detail it removes
+ * <li>all synonym relationship to the given taxon or to all taxa if taxon is <code>null</code></li>
+ * <li>the synonym concept if it is not referenced by any synonym relationship anymore</li>
+ * <BR><BR>
+ * If <code>config.removeNameIfPossible</code> 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, ...)<BR><BR>
+ * If <code>config.newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name is not deleted and
+ * the name is homotypic to the taxon the name is moved to a new homotypical group.<BR><BR>
+ *
+ * If synonym is <code>null</code> the method has no effect.
+ *
+ * @param taxon
+ * @param synonym
+ * @param config
+ * @return deleteResult
+ */
+ DeleteResult deleteSynonym(Synonym synonym, Taxon taxon,
+ SynonymDeletionConfigurator config);
+
+ public Pager<Taxon> pageAcceptedTaxaFor(UUID synonymUuid, UUID classificationUuid, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
+ List<String> propertyPaths);
+
+ public List<Taxon> listAcceptedTaxaFor(UUID synonymUuid, UUID classificationUuid, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
+ List<String> propertyPaths);
+
+ public List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config);
+
+
+
BGBM BDI Projects / cdmlib.git / blobdiff