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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.persistence.dao.taxon;
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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.hibernate.criterion.Criterion;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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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.SynonymType;
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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.model.term.DefinedTerm;
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import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao;
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import eu.etaxonomy.cdm.persistence.dao.common.IPublishableDao;
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import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.NameSearchOrder;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.persistence.query.TaxonTitleType;
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/**
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* @author a.mueller
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*
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*/
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public interface ITaxonDao
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extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase>, IPublishableDao<TaxonBase> {
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/**
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* {@inheritDoc}
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* <BR><BR>
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* NOTE: Also taxa with <code>publish=false</code> are returned.
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*/
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@Override
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public TaxonBase load(UUID uuid, List<String> propertyPaths);
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/**
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* Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter,
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* and taxon.sec matches the sec parameter.
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* @param name
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* @param sec
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* @return
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*/
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public List<TaxonBase> getTaxaByName(String name, boolean includeUnpublished, Reference sec);
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/**
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* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
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* where the taxonBase.name.nameCache property matches the String queryString, and taxon.sec matches the sec parameter.
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* @param name
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* @param sec
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* @return
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*/
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public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, boolean includeUnpublished, Reference sec);
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/**
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* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
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* where the taxonBase.name.nameCache property matches the String queryString.
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* @param queryString
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* @param matchMode
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* @param accepted
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* @param pageSize
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* @param pageNumber
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* @return
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*/
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public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode,
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Boolean accepted, boolean includeUnpublished, Integer pageSize, Integer pageNumber);
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/**
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* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
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* where the taxonBase.name.nameCache property matches the String queryString.
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* @param doTaxa
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* @param doSynonyms
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* @param queryString
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* @param classification TODO
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* @param subtree
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* @param matchMode
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* @param namedAreas TODO
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* @param pageSize
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* @param pageNumber
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* @param propertyPaths TODO
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* @return list of found taxa
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*/
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public List<TaxonBase> getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
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boolean includeAuthors, String queryString, Classification classification, TaxonNode subtree,
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MatchMode matchMode, Set<NamedArea> namedAreas, boolean includeUnpublished,
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NameSearchOrder order, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* @param doTaxa
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* @param doSynonyms
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* @param queryString
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* @param classification TODO
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* @param subtree
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* @param matchMode
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* @param namedAreas
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* @param pageSize
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* @param pageNumber
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* @param propertyPaths
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* @return
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*/
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public long countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, boolean doCommonNames,
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boolean doIncludeAuthors, String queryString, Classification classification, TaxonNode subtree,
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MatchMode matchMode, Set<NamedArea> namedAreas, boolean includeUnpublished);
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/**
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* Returns a count of TaxonBase instances where the
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* taxon.name properties match the parameters passed.
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*
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* @param doTaxa
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* @param doSynonyms
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* @param uninomial
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* @param infragenericEpithet
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* @param specificEpithet
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* @param infraspecificEpithet
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* @param rank
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* @return a count of TaxonBase instances
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*/
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public long countTaxaByName(Class <? extends TaxonBase> clazz, String uninomial, String infragenericEpithet,String specificEpithet, String infraspecificEpithet, Rank rank);
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/**
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* Returns a list of TaxonBase instances where the
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* taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
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* <i>null</i> will search for those taxa with a value of null in that field
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* <p>
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* Compare with
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* {@link #findByName(String, MatchMode, int, int, boolean)}
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* which searches for {@link TaxonName}<strong><code>.titleCache</code>
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* </strong>
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*
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* @param doTaxa
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* @param doSynonyms
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* @param uninomial
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* @param infragenericEpithet
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* @param specificEpithet
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* @param infraspecificEpithet
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* @param rank
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* @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
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* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @return a list of TaxonBase instances
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*/
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public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
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/**
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* Find taxa by searching for Taxa and Synonyms where the
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* {@link TaxonName}<strong><code>.titleCache</code></strong> matches
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* the name specified as queryString <code>taxonName</code>
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* <P>
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* Compare with
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* {@link #findTaxaByName(Class, String, String, String, String, Rank, Integer, Integer)}
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* which searches for {@link TaxonName}<strong><code>.nameCache</code>
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* </strong>
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* @param queryString
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* the taqxon Name to search for
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* @param classification TODO
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* @param matchMode
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* @param namedAreas TODO
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* @param pageNumber
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* @param pageSize
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* @param onlyAcccepted
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* @return
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*/
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public List<TaxonBase> findByNameTitleCache(boolean doTaxa, boolean doSynonyms, boolean includeUnpublished,
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String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, Set<NamedArea> namedAreas,
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NameSearchOrder order, Integer pageNumber, Integer pageSize, List<String> propertyPaths) ;
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/**
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* Returns a taxon corresponding to the given uuid
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*
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* @param uuid
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* The uuid of the taxon requested
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* @param criteria
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* Custom criteria to be added to the default list of applied criteria.
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* @param propertyPaths
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*
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* @return
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*/
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public TaxonBase findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths);
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/**
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* Returns a list of Taxon entities corresponding to the given uuid list.
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* @param uuids
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* @param criteria
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* @param propertyPaths
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* @return
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*/
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public List<? extends TaxonBase> findByUuids(List<UUID> uuids, List<Criterion> criteria, List<String> propertyPaths);
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/**
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* @param queryString
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* @param classification
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* @param matchMode
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* @param namedAreas
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* @param pageSize
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* @param pageNumber
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* @param propertyPaths
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* @return A List matching Taxa
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*/
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public List<Taxon> getTaxaByCommonName(String queryString, Classification classification,
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MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize,
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Integer pageNumber, List<String> propertyPaths);
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/**
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* Counts the number of synonyms
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* @param onlyAttachedToTaxon if <code>true</code> only those synonyms being attached to
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* an accepted taxon are counted
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* @return the number of synonyms
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*/
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public long countSynonyms(boolean onlyAttachedToTaxon);
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/**
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* @param queryString
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* @param matchMode
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* @param onlyAcccepted
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* @return
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*/
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public long countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted);
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/**
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* @param queryString
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* @param matchMode
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* @param onlyAcccepted
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* @param criteria
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* @return
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*/
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public long countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria);
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/**
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* Returns a count of the TaxonRelationships (of where relationship.type ==
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* type, if this argument is supplied) where the supplied taxon either is
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* relatedFrom or relatedTo depending on the <code>direction</code>
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* parameter.
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*
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* @param taxon
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* The taxon that is relatedFrom
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* @param type
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* The type of TaxonRelationship (can be null)
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* @param direction
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* specifies the direction of the relationship
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* @return the number of TaxonRelationship instances
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*/
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public long countTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
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boolean includeUnpublished, Direction direction);
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public long countTaxonRelationships(Taxon taxon, Set<TaxonRelationshipType> types,
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boolean includeUnpublished, Direction direction);
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/**
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* Returns the TaxonRelationships (of where relationship.type == type, if
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* this argument is supplied) where the supplied taxon either is
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* relatedFrom or relatedTo depending on the <code>direction</code>
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* parameter.
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*
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* @param taxon
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* The taxon that is relatedTo
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* @param type
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* The type of TaxonRelationship (can be null)
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* @param pageSize
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* The maximum number of relationships returned (can be null for
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* all relationships)
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* @param pageNumber
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* The offset (in pageSize chunks) from the start of the result
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* set (0 - based)
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* @param orderHints
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* Properties to order by
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* @param propertyPaths
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* Properties to initialize in the returned entities, following
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* the syntax described in
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* {@link IBeanInitializer#initialize(Object, List)}
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* @param direction
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* specifies the direction of the relationship
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* @return a List of TaxonRelationship instances
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*/
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public List<TaxonRelationship> getTaxonRelationships(Taxon taxon,
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TaxonRelationshipType type, boolean includeUnpublished,
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Integer pageSize, Integer pageNumber,
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List<OrderHint> orderHints, List<String> propertyPaths,
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Direction direction);
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public List<TaxonRelationship> getTaxonRelationships(Taxon taxon,
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Set<TaxonRelationshipType> type, boolean includeUnpublished,
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Integer pageSize, Integer pageNumber,
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List<OrderHint> orderHints, List<String> propertyPaths,
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Direction direction);
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/**
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* Returns a count of the Synonyms (where relationship.type == type,
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* if this argument is supplied) 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 Synonym (can be null)
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* @return the number of Synonym instances
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*/
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public long countSynonyms(Taxon taxon, SynonymType type);
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/**
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* Returns the Synonyms (of where relationship.type == type, if this argument is supplied)
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* that do have the supplied taxon as accepted taxon.
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*
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* @param taxon The accepted taxon
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* @param type The type of synonym (can be null)
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* @param pageSize The maximum number of synonyms returned (can be null for all synonyms)
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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 {@link List} of {@link Synonym} instances
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*/
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public List<Synonym> getSynonyms(Taxon taxon, SynonymType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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* Returns a count of the synonyms (where relationship.type == type,
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* if this argument is supplied) which do have an accepted taxon.
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*
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* @param synonym The synonym that is relatedFrom
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* @param type The type of Synonym (can be null)
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* @return the number of Synonym instances
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*/
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public long countSynonyms(Synonym synonym, SynonymType type);
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public List<TaxonName> findIdenticalTaxonNames(List<String> propertyPath);
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public long countTaxaByCommonName(String searchString,
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Classification classification, MatchMode matchMode,
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Set<NamedArea> namedAreas);
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public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPath);
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public List<TaxonName> findIdenticalNamesNew(List <String> propertyPaths);
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public List<UuidAndTitleCache<? extends IdentifiableEntity>> getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doNamesWithoutTaxa,
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boolean doMisappliedNames, boolean doCommonNames, boolean includeUnpublished,
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String queryString, Classification classification, TaxonNode subtree,
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MatchMode matchMode, Set<NamedArea> namedAreas, NameSearchOrder order);
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public List<String> taxaByNameNotInDB(List<String> taxonNames);
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/**
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* This method was originally required when synonyms still had a synonym relationship
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* to taxa and could belong to multiple taxa. Now the method might be obsolete.
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* @param synonym
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* @param classificationFilter
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* @param propertyPaths
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* @see #countAcceptedTaxonFor(Synonym, Classification)
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*/
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public Taxon acceptedTaxonFor(Synonym synonym, Classification classificationFilter, List<String> propertyPaths);
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/**
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* This method was originally required when synonyms still had a synonym relationship
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* to taxa and could belong to multiple taxa. Now the method might be obsolete.@param synonym
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* @param classificationFilter
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*
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* @see #acceptedTaxonFor(Synonym, Classification, Integer, Integer, List, List)
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*/
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public long countAcceptedTaxonFor(Synonym synonym, Classification classificationFilter);
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public List<UuidAndTitleCache<Taxon>> getTaxaByCommonNameForEditor(
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String titleSearchStringSqlized, Classification classification,
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MatchMode matchMode, Set<NamedArea> namedAreas);
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public <S extends TaxonBase> List<Object[]> findByIdentifier(Class<S> clazz, String identifier,
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DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode,
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boolean includeEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
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/**
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* Counts all taxa which match the given identifier (identifier type, identifier string and match mode).
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* Optionally a subtreefilter can be defined.
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*
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* @param clazz optional, the TaxonBase subclass
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* @param identifier the identifier string
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* @param identifierType the identifier type
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* @param matchmode the match mode for the identifier string
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* @param subtreeFilter the subtree filter as taxon node
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* @return
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*/
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public <S extends TaxonBase> long countByIdentifier(Class<S> clazz,
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String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode);
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/**
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401
|
* Counts all taxa which have the given marker of type markerType and with value markerValue.
|
402
|
* Additionally an optional subtreefilter can be defined.
|
403
|
*
|
404
|
* @param clazz
|
405
|
* @param markerType
|
406
|
* @param markerValue
|
407
|
* @param subtreeFilter
|
408
|
* @return
|
409
|
*/
|
410
|
public <S extends TaxonBase> long countByMarker(Class<S> clazz, MarkerType markerType,
|
411
|
Boolean markerValue, TaxonNode subtreeFilter);
|
412
|
|
413
|
/**
|
414
|
* @param clazz
|
415
|
* @param markerType
|
416
|
* @param markerValue
|
417
|
* @param subtreeFilter
|
418
|
* @param includeEntity
|
419
|
* @param pageSize
|
420
|
* @param pageNumber
|
421
|
* @param propertyPaths
|
422
|
* @return
|
423
|
*/
|
424
|
public <S extends TaxonBase> List<Object[]> findByMarker(Class<S> clazz, MarkerType markerType,
|
425
|
Boolean markerValue, TaxonNode subtreeFilter, boolean includeEntity, TaxonTitleType titleType,
|
426
|
Integer pageSize, Integer pageNumber, List<String> propertyPaths);
|
427
|
|
428
|
|
429
|
/**
|
430
|
* @param types
|
431
|
* @return
|
432
|
*/
|
433
|
public long countTaxonRelationships(Set<TaxonRelationshipType> types);
|
434
|
|
435
|
/**
|
436
|
* @param types
|
437
|
* @param pageSize
|
438
|
* @param pageNumber
|
439
|
* @param orderHints
|
440
|
* @param propertyPaths
|
441
|
* @return
|
442
|
*/
|
443
|
public List<TaxonRelationship> getTaxonRelationships(Set<TaxonRelationshipType> types,
|
444
|
Integer pageSize, Integer pageNumber,
|
445
|
List<OrderHint> orderHints, List<String> propertyPaths);
|
446
|
|
447
|
|
448
|
|
449
|
}
|