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// $Id$
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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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import java.io.IOException;
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import java.util.EnumSet;
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import java.util.List;
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import java.util.Set;
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import java.util.UUID;
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import org.apache.lucene.index.CorruptIndexException;
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import org.apache.lucene.queryparser.classic.ParseException;
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import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
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import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration;
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import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
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import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.dto.FindByIdentifierDTO;
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import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO;
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import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;
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import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;
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import eu.etaxonomy.cdm.api.service.search.SearchResult;
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import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
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import eu.etaxonomy.cdm.model.common.DefinedTerm;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Language;
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import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
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import eu.etaxonomy.cdm.model.common.RelationshipBase;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.Feature;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.media.Media;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonNameBase;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
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import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
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/**
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* Computes all Taxon instances that do not have a taxonomic parent.
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* @param sec The concept reference that the taxon belongs to
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*
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* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
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* @return The List<Taxon> of root taxa.
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* @deprecated obsolete when using classification
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*/
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@Deprecated
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public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren);
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/**
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* Computes all Taxon instances which name is of a certain Rank.
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* @param rank The rank of the taxon name
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* @param sec The concept reference that the taxon belongs to
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* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
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* @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
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* the misapplied name are not returned.<Br>Default: true.
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* @param propertyPaths
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* properties to be initialized, For detailed description and
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* examples <b>please refer to:</b>
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* {@link IBeanInitializer#initialize(Object, List)}. <Br>
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* Default: true.
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* @return The List<Taxon> of root taxa.
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* @deprecated obsolete when using classification
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*/
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@Deprecated
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public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
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/**
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* Computes all relationships.
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* @param limit
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* @param start
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* @return
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* FIXME candidate for harmonization - rename to listRelationships
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*/
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public List<RelationshipBase> getAllRelationships(int limit, int start);
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/**
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* Returns TaxonRelationshipType vocabulary
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* @return
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* @deprecated use TermService#getVocabulary(VocabularyType) instead
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*/
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@Deprecated
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public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
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/**
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* Returns a list of taxa that matches the name string and the sec reference
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* @param name the name string to search for
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* @param sec the taxons sec reference
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* @return a list of taxa matching the name and the sec reference
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*/
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public List<TaxonBase> searchTaxaByName(String name, Reference sec);
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/**
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* Swaps given synonym and accepted taxon.
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* In particular:
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* <ul>
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* <li>A new accepted taxon with the synonyms name is created</li>
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* <li>The synonym is deleted from the old accepted taxons synonym list</li>
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* <li>A new synonym with the name of the old accepted taxon is created</li>
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* <li>The newly created synonym get related to the newly created accepted taxon</li>
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* </ul>
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*
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* @param synonym
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* @param acceptedTaxon
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* @param synonymRelationshipType the relationship type the newly created synonym will have. Defaults to SYNONYM_OF
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* @return
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*/
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public UpdateResult swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
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/**
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* Changes a synonym into an accepted taxon and removes
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* the synonym relationship to the given accepted taxon.
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* Other synonyms homotypic to the synonym to change are
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* moved to the same new accepted taxon as homotypic
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* synonyms. The new accepted taxon has the same name and
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* the same sec reference as the old synonym.<BR>
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* If the given accepted taxon and the synonym are homotypic
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* to each other an exception may be thrown as taxonomically it doesn't
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* make sense to have two accepted taxa in the same homotypic group
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* but also it is than difficult to decide how to handle other names
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* in the homotypic group. It is up to the implementing class to
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* handle this situation via an exception or in another way.
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*
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*
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* @param synonym
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* the synonym to change into an accepted taxon
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* @param acceptedTaxon
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* an accepted taxon, the synonym had a relationship to
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* @param deleteSynonym
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* if true the method tries to delete the old synonym from the database
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* @param copyCitationInfo
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* if true the citation and the microcitation of newly created synonyms
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* is taken from the old synonym relationships.
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* @param citation
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* if given this citation is added to the newly created synonym
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* relationships as citation. Only used if copyCitationInfo is <code> false</code>
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* @param microCitation
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* if given this microCitation is added to the newly created synonym
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* relationships as microCitation.Only used if copyCitationInfo is <code> false</code>
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* @return
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* the newly created accepted taxon
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* @throws IllegalArgumentException
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* if the given accepted taxon and the synonym are homotypic
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* to each other an exception may be thrown as taxonomically it doesn't
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* make sense to have two accepted taxa in the same homotypic group
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* but also it is than difficult to decide how to handle other names
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* in the homotypic group. It is up to the implementing class to
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* handle this situation via an exception or in another way.
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*/
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public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws HomotypicalGroupChangeException;
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/**
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* TODO still needed and correct?
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* Change a synonym into a related concept
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*
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* @param synonym
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* the synonym to change into the concept taxon
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* @param toTaxon
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* the taxon the newly created concept should be related to
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* @param taxonRelationshipType
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* the type of relationship
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* @param reference
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* @param microReference
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* @return
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* the newly created concept
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*/
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public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference reference, String microReference);
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/**
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* TODO still needed and correct?
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* Change a synonym into a related concept
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*
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* @param synonym
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* the synonym to change into the concept taxon
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* @param toTaxon
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* the taxon the newly created concept should be related to
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* @param taxonRelationshipType
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* the type of relationship
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* @param reference
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* @param microReference
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* @return
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* the newly created concept
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* @throws DataChangeNoRollbackException
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*/
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public Synonym changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon,
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TaxonRelationshipType oldRelationshipType,
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SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException;
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/**
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* Deletes all synonym relationships of a given synonym. If taxon is given
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* only those relationships to the taxon are deleted.
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*
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* @param syn
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* the synonym
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* @param taxon
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* @return
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* @deprecated This method must no longer being used since the
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* SynonymRelationship is annotated at the {@link Taxon} and at
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* the {@link Synonym} with <code>orphanDelete=true</code>. Just
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* remove the from and to entities from the relationship and
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* hibernate will care for the deletion. Using this method can cause
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* <code>StaleStateException</code> (see http://dev.e-taxonomy.eu/trac/ticket/3797)
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*
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*/
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@Deprecated
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public long deleteSynonymRelationships(Synonym syn, Taxon taxon);
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/**
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* Changes the homotypic group of a synonym into the new homotypic group.
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* All relations to taxa are updated correctly depending on the homotypic
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* group of the accepted taxon. <BR>
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* All existing basionym relationships to and from this name are removed.<BR>
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* If the parameter <code>targetTaxon</code> is defined, the synonym is
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* added to this taxon irrespctive of if it has been related to this
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* taxon before.<BR>
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* If <code>removeFromOtherTaxa</code> is true and <code>targetTaxon</code> is
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* defined all relationships to other taxa are deleted.<BR>
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* If <code>setBasionymRelationIfApplicable</code> is true a basionym relationship
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* between the existing basionym(s) of the new homotypic group and the synonyms name
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* is added.<BR>
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*
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* @param synonym
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* @param newHomotypicalGroup
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* @param taxon
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* @param setBasionymRelationIfApplicable
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*/
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public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
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boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable);
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/**
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* Moves a synonym to another taxon and removes the old synonym relationship.
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*
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* @param oldSynonymRelation the old synonym relationship defining the synonym to move and the old accepted taxon.
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* @param newTaxon the taxon the synonym will be moved to
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* @param moveHomotypicGroup if the synonym belongs to a homotypical group with other synonyms and
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* <code>moveHomotypicGroup</code> is <code>true</code> all these synonyms are moved to the new taxon,
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* if <code>false</code> a {@link HomotypicalGroupChangeException} is thrown.
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* <code>MoveHomotypicGroup</code> has no effect if the synonym is the only synonym in it's homotypic group.
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* @param newSynonymRelationshipType the synonym relationship type of the new synonym relations. Default is
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* {@link SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF() heterotypic}.
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* @param newReference The reference for the new synonym relation(s).
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* @param newReferenceDetail The reference detail for the new synonym relation(s).
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* @param keepReference if no <code>newReference</code> and/or no <code>newReferenceDetail</code>
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* is defined they are taken from the old synonym relation(s) if <code>keepReference</code> is
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* <code>true</code>. If <code>false</code> the reference and the reference detail will be taken
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* only from the <code>newReference</code> and <code>newReferenceDetail</code>.
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* @return The new synonym relationship. If <code>moveHomotypicGroup</code> is <code>true</code> additionally
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* created new synonym relationships must be retrieved separately from the new taxon.
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* @throws HomotypicalGroupChangeException Exception is thrown if (1) synonym is homotypic to the old accepted taxon or
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* (2) synonym is in homotypic group with other synonyms and <code>moveHomotypicGroup</code> is false
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*/
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public UpdateResult moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation, Taxon newTaxon, boolean moveHomotypicGroup,
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SynonymRelationshipType newSynonymRelationshipType, Reference newReference, String newReferenceDetail, boolean keepReference) throws HomotypicalGroupChangeException;
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
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* where the supplied taxon is relatedTo.
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*
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* @param taxon The taxon that is relatedTo
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
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* @return a List of TaxonRelationship instances
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*/
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public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
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* where the supplied taxon is relatedTo.
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*
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* @param taxon The taxon that is relatedTo
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
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* @return a Pager of TaxonRelationship instances
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*/
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public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
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* where the supplied taxon is relatedFrom.
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*
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* @param taxon The taxon that is relatedFrom
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
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* @return a List of TaxonRelationship instances
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*/
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public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
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* where the supplied taxon is relatedFrom.
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*
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* @param taxon The taxon that is relatedFrom
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* @param type The type of TaxonRelationship (can be null)
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param orderHints Properties to order by
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* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
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* @return a Pager of TaxonRelationship instances
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*/
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public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* lists all taxa which are related to the <code>taxon</code> given as
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* parameter.
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*
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* @param taxon
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* @param includeRelationships
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* @param maxDepth
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* <code>1</code> for one level, <code>null</code> for infinite
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* depth, <code>0</code> will completely omit collecting related taxa.
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* @param limit
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* @param start
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* @param propertyPaths
|
357
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* @return
|
358
|
*/
|
359
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public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,
|
360
|
Integer limit, Integer start, List<String> propertyPaths);
|
361
|
|
362
|
/**
|
363
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* lists all accepted taxa for the given {@link Synonym}
|
364
|
*
|
365
|
* @param taxonBase
|
366
|
* @param limit
|
367
|
* @param start
|
368
|
* @param propertyPaths
|
369
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* @return
|
370
|
*/
|
371
|
public List<Classification> listClassifications(TaxonBase taxonBase, Integer limit, Integer start, List<String> propertyPaths);
|
372
|
|
373
|
/**
|
374
|
* Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
|
375
|
* where the supplied synonym is relatedFrom.
|
376
|
*
|
377
|
* @param taxon The synonym that is relatedFrom
|
378
|
* @param type The type of SynonymRelationship (can be null)
|
379
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
380
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
381
|
* * @param orderHints Properties to order by
|
382
|
* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
|
383
|
* @return a Pager of SynonymRelationship instances
|
384
|
*/
|
385
|
public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
386
|
|
387
|
/**
|
388
|
* Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
|
389
|
* where the supplied taxon is relatedTo.
|
390
|
*
|
391
|
* @param taxon The taxon that is relatedTo
|
392
|
* @param type The type of SynonymRelationship (can be null)
|
393
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
394
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
395
|
* * @param orderHints Properties to order by
|
396
|
* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
|
397
|
* @return a Pager of SynonymRelationship instances
|
398
|
*/
|
399
|
public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
400
|
|
401
|
/**
|
402
|
* This method returns in the first entry the list of synonyms of the
|
403
|
* homotypic group of the accepted taxon. All other entries represent the lists of heterotypic
|
404
|
* synonym groups. For detailed information about these 2 groups see
|
405
|
* {@link #getHomotypicSynonymsByHomotypicGroup(Taxon, List)} and
|
406
|
* {@link #getHeterotypicSynonymyGroups(Taxon, List)}
|
407
|
*
|
408
|
* @see #getSynonyms()
|
409
|
* @see SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF()
|
410
|
* @see eu.etaxonomy.cdm.model.name.HomotypicalGroup
|
411
|
|
412
|
* @param taxon the accepted taxon
|
413
|
* @param propertyPaths the property path
|
414
|
* @return the list of groups of synonyms
|
415
|
*/
|
416
|
public List<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
|
417
|
|
418
|
|
419
|
/**
|
420
|
* Returns the list of all synonyms that share the same homotypical group with the given taxon.
|
421
|
* Only those homotypic synonyms are returned that do have a synonym relationship with the accepted taxon.
|
422
|
* @param taxon
|
423
|
* @param propertyPaths
|
424
|
* @return
|
425
|
*/
|
426
|
public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
|
427
|
|
428
|
/**
|
429
|
* Returns the ordered list of all {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical groups}
|
430
|
* that contain {@link Synonym synonyms} that are heterotypic to the given taxon.
|
431
|
* {@link eu.etaxonomy.cdm.model.name.TaxonNameBase Taxon names} of heterotypic synonyms
|
432
|
* belong to a homotypical group which cannot be the homotypical group to which the
|
433
|
* taxon name of the given taxon belongs. This method does not return the homotypic group the given
|
434
|
* taxon belongs to.<BR>
|
435
|
* This method does neglect the type of synonym relationship that is defined between the given taxon
|
436
|
* and the synonym. So the synonym relationship may be homotypic however a synonym is returned
|
437
|
* in one of the result lists as long as the synonym does not belong to the same homotypic group as
|
438
|
* the given taxon.<BR>
|
439
|
* The list returned is ordered according to the date of publication of the
|
440
|
* first published name within each homotypical group.
|
441
|
*
|
442
|
* @see #getHeterotypicSynonymyGroups()
|
443
|
* @see #getSynonyms()
|
444
|
* @see SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF()
|
445
|
* @see eu.etaxonomy.cdm.model.name.HomotypicalGroup
|
446
|
|
447
|
* @param taxon
|
448
|
* @param propertyPaths
|
449
|
* @return
|
450
|
*/
|
451
|
public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
|
452
|
|
453
|
/**
|
454
|
* Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
|
455
|
*
|
456
|
* @param clazz filter the results by class (or pass null to return all TaxonBase instances)
|
457
|
* @param queryString
|
458
|
* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
|
459
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
460
|
* @param orderHints
|
461
|
* Supports path like <code>orderHints.propertyNames</code> which
|
462
|
* include *-to-one properties like createdBy.username or
|
463
|
* authorTeam.persistentTitleCache
|
464
|
* @param propertyPaths properties to be initialized
|
465
|
* @return a Pager Taxon instances
|
466
|
* @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
|
467
|
*/
|
468
|
@Override
|
469
|
public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
|
470
|
|
471
|
/**
|
472
|
* Returns a list of TaxonBase instances where the
|
473
|
* taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
|
474
|
* <i>null</i> will search for those taxa with a value of null in that field
|
475
|
*
|
476
|
* @param clazz optionally filter by class (can be null to return all taxa)
|
477
|
* @param uninomial
|
478
|
* @param infragenericEpithet
|
479
|
* @param specificEpithet
|
480
|
* @param infraspecificEpithet
|
481
|
* @param rank
|
482
|
* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
|
483
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
484
|
* @return a list of TaxonBase instances
|
485
|
*/
|
486
|
public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
|
487
|
|
488
|
/**
|
489
|
* Returns a list of TaxonBase instances where the
|
490
|
* taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
|
491
|
* <i>null</i> will search for those taxa with a value of null in that field
|
492
|
*
|
493
|
* @param clazz optionally filter by class
|
494
|
* @param uninomial
|
495
|
* @param infragenericEpithet
|
496
|
* @param specificEpithet
|
497
|
* @param infraspecificEpithet
|
498
|
* @param rank
|
499
|
* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
|
500
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
501
|
* @return a List of TaxonBase instances
|
502
|
*/
|
503
|
public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
|
504
|
|
505
|
/**
|
506
|
* Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)
|
507
|
* that match the properties specified in the configurator.
|
508
|
* @param configurator
|
509
|
* @return
|
510
|
*/
|
511
|
public Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator);
|
512
|
|
513
|
/**
|
514
|
* performes a union searches for TaxonBase instances on all available
|
515
|
* free text indexes. At the time of writing this documentation it combines
|
516
|
* {@link #findByDescriptionElementFullText(Class, String, Classification, List, List, boolean, Integer, Integer, List, List)}
|
517
|
* and {@link #findByFullText(Class, String, Classification, List, boolean, Integer, Integer, List, List)
|
518
|
*
|
519
|
* @param queryString
|
520
|
* the query string
|
521
|
* @param classification
|
522
|
* Additional filter criterion: If a taxonomic classification
|
523
|
* three is specified here the result set will only contain taxa
|
524
|
* of the given classification
|
525
|
* @param languages
|
526
|
* Additional filter criterion: Search only in these languages.
|
527
|
* Not all text fields in the cdm model are multilingual, thus
|
528
|
* this setting will only apply to the multilingiual fields.
|
529
|
* Other fields are searched nevertheless if this parameter is
|
530
|
* set or not.
|
531
|
* @param highlightFragments
|
532
|
* TODO
|
533
|
* @param pageSize
|
534
|
* The maximum number of objects returned (can be null for all
|
535
|
* objects)
|
536
|
* @param pageNumber
|
537
|
* The offset (in pageSize chunks) from the start of the result
|
538
|
* set (0 - based)
|
539
|
* @param orderHints
|
540
|
* Supports path like <code>orderHints.propertyNames</code> which
|
541
|
* include *-to-one properties like createdBy.username or
|
542
|
* authorTeam.persistentTitleCache
|
543
|
* @param propertyPaths
|
544
|
* properties to initialize - see
|
545
|
* {@link IBeanInitializer#initialize(Object, List)}
|
546
|
* @return a paged list of instances of type T matching the queryString and
|
547
|
* the additional filter criteria
|
548
|
* @return
|
549
|
* @throws CorruptIndexException
|
550
|
* @throws IOException
|
551
|
* @throws ParseException
|
552
|
* @throws LuceneMultiSearchException
|
553
|
* @deprecated this search should fully be covered by the new method
|
554
|
* {@link #findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List)}
|
555
|
* , maybe we should rename this latter method to give it a more meaningful name
|
556
|
*/
|
557
|
@Deprecated
|
558
|
public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,
|
559
|
Classification classification, List<Language> languages, boolean highlightFragments,
|
560
|
Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException;
|
561
|
|
562
|
/**
|
563
|
* Searches for TaxonBase instances using the TaxonBase free text index.
|
564
|
*
|
565
|
* <h4>This is an experimental feature, it may be moved, modified, or even
|
566
|
* removed in future releases!!!</h4>
|
567
|
*
|
568
|
* @param clazz
|
569
|
* Additional filter criterion: The specific TaxonBase subclass
|
570
|
* to search for
|
571
|
* @param queryString
|
572
|
* the query string
|
573
|
* @param classification
|
574
|
* Additional filter criterion: If a taxonomic classification
|
575
|
* three is specified here the result set will only contain taxa
|
576
|
* of the given classification
|
577
|
* @param languages
|
578
|
* Additional filter criterion: Search only in these languages.
|
579
|
* Not all text fields in the cdm model are multilingual, thus
|
580
|
* this setting will only apply to the multilingiual fields.
|
581
|
* Other fields are searched nevertheless if this parameter is
|
582
|
* set or not.
|
583
|
* @param highlightFragments
|
584
|
* TODO
|
585
|
* @param pageSize
|
586
|
* The maximum number of objects returned (can be null for all
|
587
|
* objects)
|
588
|
* @param pageNumber
|
589
|
* The offset (in pageSize chunks) from the start of the result
|
590
|
* set (0 - based)
|
591
|
* @param orderHints
|
592
|
* Supports path like <code>orderHints.propertyNames</code> which
|
593
|
* include *-to-one properties like createdBy.username or
|
594
|
* authorTeam.persistentTitleCache
|
595
|
* @param propertyPaths
|
596
|
* properties to initialize - see
|
597
|
* {@link IBeanInitializer#initialize(Object, List)}
|
598
|
* @return a paged list of instances of type T matching the queryString and
|
599
|
* the additional filter criteria
|
600
|
* @throws CorruptIndexException
|
601
|
* @throws IOException
|
602
|
* @throws ParseException
|
603
|
*/
|
604
|
public Pager<SearchResult<TaxonBase>> findByFullText(Class<? extends TaxonBase> clazz, String queryString, Classification classification,
|
605
|
List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
606
|
List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException;
|
607
|
|
608
|
|
609
|
/**
|
610
|
* @param areaFilter
|
611
|
* @param statusFilter
|
612
|
* @param classification
|
613
|
* Additional filter criterion: If a taxonomic classification
|
614
|
* three is specified here the result set will only contain taxa
|
615
|
* of the given classification
|
616
|
* @param highlightFragments
|
617
|
* @param pageSize
|
618
|
* The maximum number of objects returned (can be null for all
|
619
|
* objects)
|
620
|
* @param pageNumber
|
621
|
* The offset (in pageSize chunks) from the start of the result
|
622
|
* set (0 - based)
|
623
|
* @param orderHints
|
624
|
* Supports path like <code>orderHints.propertyNames</code> which
|
625
|
* include *-to-one properties like createdBy.username or
|
626
|
* authorTeam.persistentTitleCache
|
627
|
* @param propertyPath
|
628
|
* Common properties to initialize the instances of the
|
629
|
* CDM types ({@link Taxon} and {@link Synonym}
|
630
|
* this method can return - see {@link IBeanInitializer#initialize(Object, List)}
|
631
|
* @return a paged list of instances of {@link Taxon} instances
|
632
|
* @throws IOException
|
633
|
* @throws ParseException
|
634
|
*/
|
635
|
public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTerm> statusFilter,
|
636
|
Classification classification,
|
637
|
Integer pageSize, Integer pageNumber,
|
638
|
List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, ParseException;
|
639
|
|
640
|
/**
|
641
|
* Searches for TaxonBase instances using the TaxonBase free text index.
|
642
|
*
|
643
|
*
|
644
|
*
|
645
|
* <h4>This is an experimental feature, it may be moved, modified, or even
|
646
|
* removed in future releases!!!</h4>
|
647
|
* @param searchModes
|
648
|
* Additional filter criterion: defaults to [doTaxa] if set null
|
649
|
* @param queryString
|
650
|
* the query string
|
651
|
* @param classification
|
652
|
* Additional filter criterion: If a taxonomic classification
|
653
|
* three is specified here the result set will only contain taxa
|
654
|
* of the given classification
|
655
|
* @param namedAreas
|
656
|
* @param languages
|
657
|
* Additional filter criterion: Search only in these languages.
|
658
|
* Not all text fields in the cdm model are multilingual, thus
|
659
|
* this setting will only apply to the multilingiual fields.
|
660
|
* Other fields are searched nevertheless if this parameter is
|
661
|
* set or not.
|
662
|
* @param highlightFragments
|
663
|
* TODO
|
664
|
* @param pageSize
|
665
|
* The maximum number of objects returned (can be null for all
|
666
|
* objects)
|
667
|
* @param pageNumber
|
668
|
* The offset (in pageSize chunks) from the start of the result
|
669
|
* set (0 - based)
|
670
|
* @param orderHints
|
671
|
* Supports path like <code>orderHints.propertyNames</code> which
|
672
|
* include *-to-one properties like createdBy.username or
|
673
|
* authorTeam.persistentTitleCache
|
674
|
* @param propertyPath
|
675
|
* Common properties to initialize the instances of the
|
676
|
* CDM types ({@link Taxon} and {@link Synonym}
|
677
|
* this method can return - see {@link IBeanInitializer#initialize(Object, List)}
|
678
|
* @return a paged list of instances of {@link Taxon}, {@link Synonym}, matching the queryString and
|
679
|
* the additional filter criteria
|
680
|
* @throws CorruptIndexException
|
681
|
* @throws IOException
|
682
|
* @throws ParseException
|
683
|
* @throws LuceneMultiSearchException
|
684
|
*/
|
685
|
public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(
|
686
|
EnumSet<TaxaAndNamesSearchMode> searchModes,
|
687
|
String queryString, Classification classification, Set<NamedArea> namedAreas, Set<PresenceAbsenceTerm> distributionStatus,
|
688
|
List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
689
|
List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException;
|
690
|
|
691
|
/**
|
692
|
* Searches for TaxonBase instances by using the DescriptionElement free text index.
|
693
|
*
|
694
|
* <h4>This is an experimental feature, it may be moved, modified, or even
|
695
|
* removed in future releases!!!</h4>
|
696
|
*
|
697
|
* @param clazz
|
698
|
* Additional filter criterion:
|
699
|
* @param queryString
|
700
|
* the query string to filter by
|
701
|
* @param classification
|
702
|
* Additional filter criterion: If a taxonomic classification
|
703
|
* three is specified here the result set will only contain taxa
|
704
|
* of the given classification
|
705
|
* @param features
|
706
|
* TODO
|
707
|
* @param languages
|
708
|
* Additional filter criterion: Search only in these languages.
|
709
|
* Not all text fields in the cdm model are multilingual, thus
|
710
|
* this setting will only apply to the multilingiual fields.
|
711
|
* Other fields are searched nevertheless if this parameter is
|
712
|
* set or not.
|
713
|
* @param highlightFragments
|
714
|
* TODO
|
715
|
* @param pageSize
|
716
|
* The maximum number of objects returned (can be null for all
|
717
|
* objects)
|
718
|
* @param pageNumber
|
719
|
* The offset (in pageSize chunks) from the start of the result
|
720
|
* set (0 - based)
|
721
|
* @param orderHints
|
722
|
* Supports path like <code>orderHints.propertyNames</code> which
|
723
|
* include *-to-one properties like createdBy.username or
|
724
|
* authorTeam.persistentTitleCache
|
725
|
* @param propertyPaths
|
726
|
* properties to initialize - see
|
727
|
* {@link IBeanInitializer#initialize(Object, List)}
|
728
|
* @return a paged list of instances of type T matching the queryString and
|
729
|
* the additional filter criteria
|
730
|
* @throws IOException
|
731
|
* @throws CorruptIndexException
|
732
|
* @throws ParseException
|
733
|
*/
|
734
|
public Pager<SearchResult<TaxonBase>> findByDescriptionElementFullText(Class<? extends DescriptionElementBase> clazz, String queryString, Classification classification, List<Feature> features, List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException;
|
735
|
|
736
|
|
737
|
/**
|
738
|
*
|
739
|
* @param taxon
|
740
|
* @param size
|
741
|
* @param height
|
742
|
* @param widthOrDuration
|
743
|
* @param mimeTypes
|
744
|
* @return
|
745
|
*
|
746
|
* @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
|
747
|
*/
|
748
|
@Deprecated
|
749
|
public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
|
750
|
|
751
|
|
752
|
/**
|
753
|
* Lists all Media found in an any TaxonDescription associated with this
|
754
|
* taxon.
|
755
|
*
|
756
|
* @param taxon
|
757
|
* @param includeRelationships
|
758
|
* the given list of TaxonRelationshipEdges will be taken into
|
759
|
* account when retrieving media associated with the given taxon.
|
760
|
* Can be NULL.
|
761
|
* @param limitToGalleries
|
762
|
* whether to take only TaxonDescription into account which are
|
763
|
* marked as gallery
|
764
|
* @return
|
765
|
* @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
|
766
|
*/
|
767
|
@Deprecated
|
768
|
public List<Media> listTaxonDescriptionMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, List<String> propertyPath);
|
769
|
|
770
|
/**
|
771
|
* Lists all Media found in an any TaxonDescription, NameDescription,
|
772
|
* SpecimenOrObservationBase, DnaSample Chromatograms, etc. associated with this taxon.
|
773
|
*
|
774
|
* @param taxon
|
775
|
* @param includeRelationships
|
776
|
* the given list of TaxonRelationshipEdges will be taken into
|
777
|
* account when retrieving media associated with the given taxon.
|
778
|
* Can be NULL.
|
779
|
* @param limitToGalleries
|
780
|
* whether to take only descriptions into account which are
|
781
|
* marked as gallery, can be NULL
|
782
|
* @param includeTaxonDescriptions
|
783
|
* whether to take TaxonDescriptions into account, can be NULL
|
784
|
* @param includeOccurrences
|
785
|
* whether to take TaxonDescriptions into account, can be NULL
|
786
|
* @param includeTaxonNameDescriptions
|
787
|
* whether to take TaxonNameDescriptions into account, can be NULL
|
788
|
* @param propertyPath
|
789
|
* @return
|
790
|
*/
|
791
|
public List<Media> listMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
|
792
|
Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,
|
793
|
Boolean includeTaxonNameDescriptions, List<String> propertyPath);
|
794
|
|
795
|
public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
|
796
|
|
797
|
/**
|
798
|
* Returns the TaxonBase with the given UUID
|
799
|
* using the given match mode and initialization strategy
|
800
|
*
|
801
|
* @param uuid
|
802
|
* @param propertyPaths
|
803
|
* @return
|
804
|
*/
|
805
|
public TaxonBase findTaxonByUuid(UUID uuid, List<String> propertyPaths);
|
806
|
|
807
|
public int countAllRelationships();
|
808
|
|
809
|
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
|
810
|
|
811
|
public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath);
|
812
|
|
813
|
public String getPhylumName(TaxonNameBase name);
|
814
|
|
815
|
public long deleteSynonymRelationships(Synonym syn);
|
816
|
|
817
|
/**
|
818
|
* Returns all {@link Taxon taxa} which are {@link TaxonRelationshipType#CONGRUENT_TO() congruent} or
|
819
|
* {@link TaxonRelationshipType#INCLUDES() included} in the taxon represented by the given taxon uuid.
|
820
|
* The result also returns the path to these taxa represented by the uuids of
|
821
|
* the {@link TaxonRelationshipType taxon relationships types} and doubtful information.
|
822
|
* If classificationUuids is set only taxa of classifications are returned which are included
|
823
|
* in the given {@link Classification classifications}. ALso the path to these taxa may not include
|
824
|
* taxa from other classifications.
|
825
|
* @param taxonUuid uuid of the original taxon
|
826
|
* @param classificationUuids List of uuids of classifications used as a filter
|
827
|
* @param includeDoubtful set to <code>true</code> if also doubtfully included taxa should be included in the result
|
828
|
* @return a DTO which includes a list of taxa with the pathes from the original taxon to the given taxon as well
|
829
|
* as doubtful and date information. The original taxon is included in the result.
|
830
|
*/
|
831
|
public IncludedTaxaDTO listIncludedTaxa(UUID taxonUuid, IncludedTaxonConfiguration configuration);
|
832
|
|
833
|
|
834
|
/**
|
835
|
* Removes a synonym.<BR><BR>
|
836
|
*
|
837
|
* In detail it removes
|
838
|
* <li>all synonym relationship to the given taxon or to all taxa if taxon is <code>null</code></li>
|
839
|
* <li>the synonym concept if it is not referenced by any synonym relationship anymore</li>
|
840
|
* <BR><BR>
|
841
|
* If <code>removeNameIfPossible</code> is true
|
842
|
* it also removes the synonym name if it is not used in any other context
|
843
|
* (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)<BR><BR>
|
844
|
* If <code>newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name is not deleted and
|
845
|
* the name is homotypic to the taxon the name is moved to a new homotypical group.<BR><BR>
|
846
|
*
|
847
|
* If synonym is <code>null</code> the method has no effect.
|
848
|
*
|
849
|
* @param taxon
|
850
|
* @param synonym
|
851
|
* @param removeNameIfPossible
|
852
|
* @return deleteResult
|
853
|
*
|
854
|
*/
|
855
|
public DeleteResult deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config);
|
856
|
|
857
|
/**
|
858
|
* Removes a synonym.
|
859
|
*
|
860
|
* The method essentially loads the synonym and calls the
|
861
|
* {@link #deleteSynonym(Synonym, SynonymDeletionConfigurator) deleteSynonym} method
|
862
|
*
|
863
|
* @param synonymUuid
|
864
|
* @param config
|
865
|
* @return
|
866
|
*/
|
867
|
public DeleteResult deleteSynonym(UUID synonymUuid, SynonymDeletionConfigurator config);
|
868
|
|
869
|
/**
|
870
|
* Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
|
871
|
* depending on direction, where the supplied taxon is relatedTo or the supplied synonym is relatedFrom.
|
872
|
*
|
873
|
* @param taxonBase The taxon or synonym that is relatedTo or relatedFrom
|
874
|
* @param type The type of SynonymRelationship (can be null)
|
875
|
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
|
876
|
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
|
877
|
* @param orderHints Properties to order by
|
878
|
* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
|
879
|
* @param direction The direction of the relationship
|
880
|
* @return a List of SynonymRelationship instances
|
881
|
*/
|
882
|
public List<SynonymRelationship> listSynonymRelationships(
|
883
|
TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
|
884
|
List<OrderHint> orderHints, List<String> propertyPaths, Direction direction);
|
885
|
|
886
|
/**
|
887
|
* @param tnb
|
888
|
* @return
|
889
|
*/
|
890
|
public Taxon findBestMatchingTaxon(String taxonName);
|
891
|
|
892
|
public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config);
|
893
|
|
894
|
public Synonym findBestMatchingSynonym(String taxonName);
|
895
|
|
896
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon(Integer limit, String pattern);
|
897
|
|
898
|
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym(Integer limit, String pattern);
|
899
|
|
900
|
public List<UuidAndTitleCache<IdentifiableEntity>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator);
|
901
|
|
902
|
/**
|
903
|
* Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
|
904
|
* @param taxon
|
905
|
* @param tree
|
906
|
* @return list of inferred synonyms
|
907
|
*/
|
908
|
public List<Synonym> createInferredSynonyms(Taxon taxon, Classification tree, SynonymRelationshipType type, boolean doWithMisappliedNames);
|
909
|
|
910
|
/**
|
911
|
* Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database
|
912
|
* @param taxon
|
913
|
* @param tree
|
914
|
* @param iDatabase
|
915
|
* @return list of inferred synonyms
|
916
|
*/
|
917
|
public List<Synonym> createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames);
|
918
|
|
919
|
|
920
|
|
921
|
|
922
|
/**
|
923
|
* Removes a synonym.<BR><BR>
|
924
|
*
|
925
|
* In detail it removes
|
926
|
* <li>all synonym relationship to the given taxon or to all taxa if taxon is <code>null</code></li>
|
927
|
* <li>the synonym concept if it is not referenced by any synonym relationship anymore</li>
|
928
|
* <BR><BR>
|
929
|
* If <code>config.removeNameIfPossible</code> is true
|
930
|
* it also removes the synonym name if it is not used in any other context
|
931
|
* (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)<BR><BR>
|
932
|
* If <code>config.newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name is not deleted and
|
933
|
* the name is homotypic to the taxon the name is moved to a new homotypical group.<BR><BR>
|
934
|
*
|
935
|
* If synonym is <code>null</code> the method has no effect.
|
936
|
*
|
937
|
* @param taxon
|
938
|
* @param synonym
|
939
|
* @param config
|
940
|
* @return deleteResult
|
941
|
*/
|
942
|
public DeleteResult deleteSynonym(Synonym synonym, Taxon taxon, SynonymDeletionConfigurator config);
|
943
|
|
944
|
|
945
|
|
946
|
public Pager<Taxon> pageAcceptedTaxaFor(UUID synonymUuid, UUID classificationUuid, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
947
|
List<String> propertyPaths);
|
948
|
|
949
|
public List<Taxon> listAcceptedTaxaFor(UUID synonymUuid, UUID classificationUuid, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
|
950
|
List<String> propertyPaths);
|
951
|
|
952
|
public List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config);
|
953
|
|
954
|
|
955
|
public <S extends TaxonBase> Pager<FindByIdentifierDTO<S>> findByIdentifier(
|
956
|
Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,
|
957
|
MatchMode matchmode, boolean includeEntity, Integer pageSize,
|
958
|
Integer pageNumber, List<String> propertyPaths);
|
959
|
|
960
|
|
961
|
/**
|
962
|
* @param synonymUuid
|
963
|
* @param taxonUuid
|
964
|
* @param config
|
965
|
* @return
|
966
|
*/
|
967
|
public DeleteResult deleteSynonym(UUID synonymUuid, UUID taxonUuid, SynonymDeletionConfigurator config);
|
968
|
|
969
|
/**
|
970
|
* @param synonymUUid
|
971
|
* @param acceptedTaxonUuid
|
972
|
* @return
|
973
|
*/
|
974
|
public UpdateResult swapSynonymAndAcceptedTaxon(UUID synonymUUid, UUID acceptedTaxonUuid);
|
975
|
|
976
|
/**
|
977
|
* @param taxonUuid
|
978
|
* @param config
|
979
|
* @param classificationUuid
|
980
|
* @return
|
981
|
*/
|
982
|
public DeleteResult deleteTaxon(UUID taxonUuid, TaxonDeletionConfigurator config, UUID classificationUuid);
|
983
|
|
984
|
public UpdateResult moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation,
|
985
|
UUID newTaxonUUID, boolean moveHomotypicGroup,
|
986
|
SynonymRelationshipType newSynonymRelationshipType,
|
987
|
Reference reference, String referenceDetail, boolean keepReference)
|
988
|
throws HomotypicalGroupChangeException;
|
989
|
|
990
|
public UpdateResult moveFactualDateToAnotherTaxon(UUID fromTaxonUuid,
|
991
|
UUID toTaxonUuid);
|
992
|
|
993
|
|
994
|
/**
|
995
|
* @param synonymUuid
|
996
|
* @param toTaxonUuid
|
997
|
* @param taxonRelationshipType
|
998
|
* @param citation
|
999
|
* @param microcitation
|
1000
|
* @return
|
1001
|
*/
|
1002
|
public UpdateResult changeSynonymToRelatedTaxon(UUID synonymUuid, UUID toTaxonUuid, TaxonRelationshipType taxonRelationshipType,
|
1003
|
Reference citation, String microcitation);
|
1004
|
|
1005
|
/**
|
1006
|
* @param fromTaxonUuid
|
1007
|
* @param toTaxonUuid
|
1008
|
* @param oldRelationshipType
|
1009
|
* @param synonymRelationshipType
|
1010
|
* @return
|
1011
|
* @throws DataChangeNoRollbackException
|
1012
|
*/
|
1013
|
public UpdateResult changeRelatedTaxonToSynonym(UUID fromTaxonUuid, UUID toTaxonUuid,
|
1014
|
TaxonRelationshipType oldRelationshipType, SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException;
|
1015
|
|
1016
|
/**
|
1017
|
* @param synonymUuid
|
1018
|
* @param acceptedTaxonUuid
|
1019
|
* @param newParentNodeUuid
|
1020
|
* @param deleteSynonym
|
1021
|
* @param copyCitationInfo
|
1022
|
* @param citation
|
1023
|
* @param microCitation
|
1024
|
* @return
|
1025
|
* @throws HomotypicalGroupChangeException
|
1026
|
*/
|
1027
|
public UpdateResult changeSynonymToAcceptedTaxon(UUID synonymUuid, UUID acceptedTaxonUuid, UUID newParentNodeUuid,
|
1028
|
boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation)
|
1029
|
throws HomotypicalGroupChangeException;
|
1030
|
|
1031
|
|
1032
|
|
1033
|
|
1034
|
|
1035
|
|
1036
|
|
1037
|
}
|