Revision 57f064a1
Added by Andreas Müller almost 8 years ago
cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java | ||
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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.DefinedTerm; |
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
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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.location.NamedArea; |
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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.common.IIdentifiableDao; |
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import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao; |
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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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/** |
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* @author a.mueller |
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* |
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*/ |
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public interface ITaxonDao extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase> { |
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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, 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, 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, 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 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, String queryString, Classification classification, |
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MatchMode matchMode, Set<NamedArea> namedAreas, 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 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, String queryString, Classification classification, |
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MatchMode matchMode, Set<NamedArea> namedAreas); |
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// /** |
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// * @param queryString |
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// * @param matchMode |
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// * @param accepted |
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// * @return |
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// */ |
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// public Integer countTaxaByName(String queryString, MatchMode matchMode, |
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// Boolean accepted); |
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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 queryString search string |
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// * @param matchMode way how search string shall be matched: exact, beginning, or anywhere |
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// * @param selectModel all taxon base, taxa, or synonyms |
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// */ |
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// public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode); |
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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 int 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 TaxonNameBase}<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, 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 TaxonNameBase}<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 TaxonNameBase}<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, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, 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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* Computes all Taxon instances that do not have a taxonomic parent and has at least one child. |
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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); |
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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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* @param cdmFetch not used yet !! TODO |
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* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true. |
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* @param withMisaplications if false only taxa are returned that have no isMisappliedNameFor relationship. |
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* <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, Boolean withMisapplications); |
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/** |
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* Computes all Taxon instances which name is of a certain Rank. |
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* |
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* @param rank |
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* The rank of the taxon name |
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* @param sec |
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* The concept reference that the taxon belongs to |
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* @param cdmFetch |
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* not used yet !! TODO |
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* @param onlyWithChildren |
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* if true only taxa are returned that have taxonomic children. <Br> |
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* Default: true. |
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* @param withMisaplications |
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* if false only taxa are returned that have no |
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* isMisappliedNameFor relationship. |
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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> |
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getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths); |
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/** |
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* TODO necessary? |
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* @param pagesize max maximum number of returned taxa |
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* @param page page to start, with 0 being first page |
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* @return |
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*/ |
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public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page); |
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/** |
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* @param limit |
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* @param start |
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* @return |
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*/ |
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public List<Taxon> getAllTaxa(Integer limit, Integer start); |
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/** |
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* @param limit |
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* @param start |
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* @return |
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*/ |
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public List<Synonym> getAllSynonyms(Integer limit, Integer start); |
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public List<RelationshipBase> getAllRelationships(Integer limit, Integer start); |
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public int countAllRelationships(); |
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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 int 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 int 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 int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, |
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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, 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 SynonymRelationships (of where relationship.type == type, |
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* if this arguement 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 SynonymRelationship (can be null) |
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* @return the number of SynonymRelationship instances |
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*/ |
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public int countSynonyms(Taxon taxon, SynonymRelationshipType type); |
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/** |
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* Returns the SynonymRelationships (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 SynonymRelationship (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 SynonymRelationship instances |
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*/ |
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public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths); |
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/** |
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* Returns a count of the SynonymRelationships (of where relationship.type == type, |
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* if this arguement is supplied) where the supplied synonym is relatedFrom. |
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* |
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* @param taxon The synonym that is relatedFrom |
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* @param type The type of SynonymRelationship (can be null) |
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* @return the number of SynonymRelationship instances |
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*/ |
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public int countSynonyms(Synonym synonym, SynonymRelationshipType type); |
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/** |
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* Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) |
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* where the supplied synonym is relatedFrom. |
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* |
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* @param taxon The synonym that is relatedFrom |
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* @param type The type of SynonymRelationship (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 SynonymRelationship instances |
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*/ |
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public List<SynonymRelationship> getSynonyms(Synonym synoynm, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths); |
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/** |
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* |
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* @return |
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*/ |
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423 |
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification); |
|
424 |
|
|
425 |
|
|
426 |
/** |
|
427 |
* Creates all inferred synonyms for the species in the tree and insert it to the database |
|
428 |
* @param tree |
|
429 |
* @return List of inferred synonyms |
|
430 |
*/ |
|
431 |
//public List<Synonym> insertAllInferredSynonymy(Classification tree); |
|
432 |
|
|
433 |
|
|
434 |
|
|
435 |
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath); |
|
436 |
public String getPhylumName(TaxonNameBase name); |
|
437 |
|
|
438 |
public long countTaxaByCommonName(String searchString, |
|
439 |
Classification classification, MatchMode matchMode, |
|
440 |
Set<NamedArea> namedAreas); |
|
441 |
|
|
442 |
/** |
|
443 |
* Deletes all synonym relationships of a given synonym. |
|
444 |
* If taxon is given only those relationships to the taxon |
|
445 |
* are deleted. |
|
446 |
* @param synonym the synonym |
|
447 |
* @param taxon the taxon, may be <code>null</code> |
|
448 |
* @return |
|
449 |
* @deprecated This method must no longer being used since the |
|
450 |
* SynonymRelationship is annotated at the {@link Taxon} and at |
|
451 |
* the {@link Synonym} with <code>orphanDelete=true</code>. Just |
|
452 |
* remove the from and to entities from the relationship and |
|
453 |
* hibernate will care for the deletion. Using this method can cause |
|
454 |
* <code>StaleStateException</code> (see http://dev.e-taxonomy.eu/trac/ticket/3797) |
|
455 |
*/ |
|
456 |
@Deprecated |
|
457 |
public long deleteSynonymRelationships(Synonym syn, Taxon taxon); |
|
458 |
|
|
459 |
public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPath); |
|
460 |
|
|
461 |
public List<TaxonNameBase> findIdenticalNamesNew(List <String> propertyPaths); |
|
462 |
|
|
463 |
|
|
464 |
public Integer countSynonymRelationships(TaxonBase taxonBase, |
|
465 |
SynonymRelationshipType type, Direction relatedfrom); |
|
466 |
|
|
467 |
public List<SynonymRelationship> getSynonymRelationships(TaxonBase taxonBase, |
|
468 |
SynonymRelationshipType type, Integer pageSize, Integer pageNumber, |
|
469 |
List<OrderHint> orderHints, List<String> propertyPaths, |
|
470 |
Direction relatedfrom); |
|
471 |
|
|
472 |
/** |
|
473 |
* @return |
|
474 |
*/ |
|
475 |
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon(Integer limit, String pattern); |
|
476 |
|
|
477 |
/** |
|
478 |
* @return |
|
479 |
*/ |
|
480 |
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym(Integer limit, String pattern); |
|
481 |
|
|
482 |
public List<UuidAndTitleCache<IdentifiableEntity>> getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doNamesWithoutTaxa, boolean doMisappliedNames, String queryString, Classification classification, |
|
483 |
MatchMode matchMode, Set<NamedArea> namedAreas); |
|
484 |
|
|
485 |
public List<String> taxaByNameNotInDB(List<String> taxonNames); |
|
486 |
|
|
487 |
public List<Taxon> listAcceptedTaxaFor(Synonym synonym, Classification classificationFilter, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, |
|
488 |
List<String> propertyPaths); |
|
489 |
|
|
490 |
public long countAcceptedTaxaFor(Synonym synonym, Classification classificationFilter); |
|
491 |
|
|
492 |
public List<UuidAndTitleCache<IdentifiableEntity>> getTaxaByCommonNameForEditor( |
|
493 |
String titleSearchStringSqlized, Classification classification, |
|
494 |
MatchMode matchMode, Set namedAreas); |
|
495 |
|
|
496 |
public <S extends TaxonBase> List<Object[]> findByIdentifier(Class<S> clazz, String identifier, |
|
497 |
DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode, |
|
498 |
boolean includeEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths); |
|
499 |
|
|
500 |
public <S extends TaxonBase> int countByIdentifier(Class<S> clazz, |
|
501 |
String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode); |
|
502 |
|
|
503 |
/** |
|
504 |
* @param classification |
|
505 |
* @param excludeUuid |
|
506 |
* @return |
|
507 |
*/ |
|
508 |
List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification( |
|
509 |
Classification classification, List<UUID> excludeUuid); |
|
510 |
|
|
511 |
/** |
|
512 |
* @param classification |
|
513 |
* @param excludeUuid |
|
514 |
* @param limit |
|
515 |
* @param pattern |
|
516 |
* @return |
|
517 |
*/ |
|
518 |
List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification( |
|
519 |
Classification classification, List<UUID> excludeUuid, Integer limit, String pattern); |
|
520 |
|
|
521 |
} |
|
1 |
/** |
|
2 |
* Copyright (C) 2007 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
|
|
10 |
package eu.etaxonomy.cdm.persistence.dao.taxon; |
|
11 |
|
|
12 |
import java.util.List; |
|
13 |
import java.util.Set; |
|
14 |
import java.util.UUID; |
|
15 |
|
|
16 |
import org.hibernate.criterion.Criterion; |
|
17 |
|
|
18 |
import eu.etaxonomy.cdm.model.common.DefinedTerm; |
|
19 |
import eu.etaxonomy.cdm.model.common.IdentifiableEntity; |
|
20 |
import eu.etaxonomy.cdm.model.common.RelationshipBase; |
|
21 |
import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction; |
|
22 |
import eu.etaxonomy.cdm.model.location.NamedArea; |
|
23 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
24 |
import eu.etaxonomy.cdm.model.name.TaxonNameBase; |
|
25 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
26 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
|
27 |
import eu.etaxonomy.cdm.model.taxon.Synonym; |
|
28 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationship; |
|
29 |
import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType; |
|
30 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
31 |
import eu.etaxonomy.cdm.model.taxon.TaxonBase; |
|
32 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
|
33 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationship; |
|
34 |
import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType; |
|
35 |
import eu.etaxonomy.cdm.persistence.dao.common.IIdentifiableDao; |
|
36 |
import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao; |
|
37 |
import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer; |
|
38 |
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache; |
|
39 |
import eu.etaxonomy.cdm.persistence.fetch.CdmFetch; |
|
40 |
import eu.etaxonomy.cdm.persistence.query.MatchMode; |
|
41 |
import eu.etaxonomy.cdm.persistence.query.OrderHint; |
|
42 |
|
|
43 |
/** |
|
44 |
* @author a.mueller |
|
45 |
* |
|
46 |
*/ |
|
47 |
public interface ITaxonDao extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase> { |
|
48 |
|
|
49 |
/** |
|
50 |
* Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter, |
|
51 |
* and taxon.sec matches the sec parameter. |
|
52 |
* @param name |
|
53 |
* @param sec |
|
54 |
* @return |
|
55 |
*/ |
|
56 |
public List<TaxonBase> getTaxaByName(String name, Reference sec); |
|
57 |
|
|
58 |
/** |
|
59 |
* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false) |
|
60 |
* where the taxonBase.name.nameCache property matches the String queryString, and taxon.sec matches the sec parameter. |
|
61 |
* @param name |
|
62 |
* @param sec |
|
63 |
* @return |
|
64 |
*/ |
|
65 |
public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, Reference sec); |
|
66 |
|
|
67 |
/** |
|
68 |
* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false) |
|
69 |
* where the taxonBase.name.nameCache property matches the String queryString. |
|
70 |
* @param queryString |
|
71 |
* @param matchMode |
|
72 |
* @param accepted |
|
73 |
* @param pageSize |
|
74 |
* @param pageNumber |
|
75 |
* @return |
|
76 |
*/ |
|
77 |
public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode, |
|
78 |
Boolean accepted, Integer pageSize, Integer pageNumber); |
|
79 |
|
|
80 |
|
|
81 |
/** |
|
82 |
* Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false) |
|
83 |
* where the taxonBase.name.nameCache property matches the String queryString. |
|
84 |
* @param doTaxa |
|
85 |
* @param doSynonyms |
|
86 |
* @param queryString |
|
87 |
* @param classification TODO |
|
88 |
* @param matchMode |
|
89 |
* @param namedAreas TODO |
|
90 |
* @param pageSize |
|
91 |
* @param pageNumber |
|
92 |
* @param propertyPaths TODO |
|
93 |
* @return list of found taxa |
|
94 |
*/ |
|
95 |
public List<TaxonBase> getTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, String queryString, Classification classification, |
|
96 |
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, List<String> propertyPaths); |
|
97 |
|
|
98 |
/** |
|
99 |
* @param doTaxa |
|
100 |
* @param doSynonyms |
|
101 |
* @param queryString |
|
102 |
* @param classification TODO |
|
103 |
* @param matchMode |
|
104 |
* @param namedAreas |
|
105 |
* @param pageSize |
|
106 |
* @param pageNumber |
|
107 |
* @param propertyPaths |
|
108 |
* @return |
|
109 |
*/ |
|
110 |
public long countTaxaByName(boolean doTaxa, boolean doSynonyms, boolean doMisappliedNames, String queryString, Classification classification, |
|
111 |
|
|
112 |
MatchMode matchMode, Set<NamedArea> namedAreas); |
|
113 |
|
|
114 |
// /** |
|
115 |
// * @param queryString |
|
116 |
// * @param matchMode |
|
117 |
// * @param accepted |
|
118 |
// * @return |
|
119 |
// */ |
|
120 |
// public Integer countTaxaByName(String queryString, MatchMode matchMode, |
|
121 |
// Boolean accepted); |
|
122 |
|
|
123 |
// /** |
|
124 |
// * Returns a count of TaxonBase instances where the |
|
125 |
// * taxon.name properties match the parameters passed. |
|
126 |
// * |
|
127 |
// * @param queryString search string |
|
128 |
// * @param matchMode way how search string shall be matched: exact, beginning, or anywhere |
|
129 |
// * @param selectModel all taxon base, taxa, or synonyms |
|
130 |
// */ |
|
131 |
// public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode); |
|
132 |
|
|
133 |
/** |
|
134 |
* Returns a count of TaxonBase instances where the |
|
135 |
* taxon.name properties match the parameters passed. |
|
136 |
* |
|
137 |
* @param doTaxa |
|
138 |
* @param doSynonyms |
|
139 |
* @param uninomial |
|
140 |
* @param infragenericEpithet |
|
141 |
* @param specificEpithet |
|
142 |
* @param infraspecificEpithet |
|
143 |
* @param rank |
|
144 |
* @return a count of TaxonBase instances |
|
145 |
*/ |
|
146 |
public int countTaxaByName(Class <? extends TaxonBase> clazz, String uninomial, String infragenericEpithet,String specificEpithet, String infraspecificEpithet, Rank rank); |
|
147 |
|
|
148 |
/** |
|
149 |
* Returns a list of TaxonBase instances where the |
|
150 |
* taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of |
|
151 |
* <i>null</i> will search for those taxa with a value of null in that field |
|
152 |
* <p> |
|
153 |
* Compare with |
|
154 |
* {@link #findByName(String, MatchMode, int, int, boolean)} |
|
155 |
* which searches for {@link TaxonNameBase}<strong><code>.titleCache</code> |
|
156 |
* </strong> |
|
157 |
* |
|
158 |
* @param doTaxa |
|
159 |
* @param doSynonyms |
|
160 |
* @param uninomial |
|
161 |
* @param infragenericEpithet |
|
162 |
* @param specificEpithet |
|
163 |
* @param infraspecificEpithet |
|
164 |
* @param rank |
|
165 |
* @param pageSize The maximum number of taxa returned (can be null for all matching taxa) |
|
166 |
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) |
|
167 |
* @return a list of TaxonBase instances |
|
168 |
*/ |
|
169 |
public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber); |
|
170 |
|
|
171 |
/** |
|
172 |
* Find taxa by searching for Taxa and Synonyms where the |
|
173 |
* {@link TaxonNameBase}<strong><code>.titleCache</code></strong> matches |
|
174 |
* the name specified as queryString <code>taxonName</code> |
|
175 |
* <P> |
|
176 |
* Compare with |
|
177 |
* {@link #findTaxaByName(Class, String, String, String, String, Rank, Integer, Integer)} |
|
178 |
* which searches for {@link TaxonNameBase}<strong><code>.nameCache</code> |
|
179 |
* </strong> |
|
180 |
* @param queryString |
|
181 |
* the taqxon Name to search for |
|
182 |
* @param classification TODO |
|
183 |
* @param matchMode |
|
184 |
* @param namedAreas TODO |
|
185 |
* @param pageNumber |
|
186 |
* @param pageSize |
|
187 |
* @param onlyAcccepted |
|
188 |
* @return |
|
189 |
*/ |
|
190 |
public List<TaxonBase> findByNameTitleCache(boolean doTaxa, boolean doSynonyms, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths) ; |
|
191 |
|
|
192 |
/** |
|
193 |
* Returns a taxon corresponding to the given uuid |
|
194 |
* |
|
195 |
* @param uuid |
|
196 |
* The uuid of the taxon requested |
|
197 |
* @param criteria |
|
198 |
* Custom criteria to be added to the default list of applied criteria. |
|
199 |
* @param propertyPaths |
|
200 |
* |
|
201 |
* @return |
|
202 |
*/ |
|
203 |
public TaxonBase findByUuid(UUID uuid, List<Criterion> criteria, List<String> propertyPaths); |
|
204 |
|
|
205 |
/** |
|
206 |
* Returns a list of Taxon entities corresponding to the given uuid list. |
|
207 |
* @param uuids |
|
208 |
* @param criteria |
|
209 |
* @param propertyPaths |
|
210 |
* @return |
|
211 |
*/ |
|
212 |
public List<? extends TaxonBase> findByUuids(List<UUID> uuids, List<Criterion> criteria, List<String> propertyPaths); |
|
213 |
|
|
214 |
/** |
|
215 |
* @param queryString |
|
216 |
* @param classification |
|
217 |
* @param matchMode |
|
218 |
* @param namedAreas |
|
219 |
* @param pageSize |
|
220 |
* @param pageNumber |
|
221 |
* @param propertyPaths |
|
222 |
* @return A List matching Taxa |
|
223 |
*/ |
|
224 |
public List<Taxon> getTaxaByCommonName(String queryString, Classification classification, |
|
225 |
MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, |
|
226 |
Integer pageNumber, List<String> propertyPaths); |
|
227 |
|
|
228 |
|
|
229 |
/** |
|
230 |
* Computes all Taxon instances that do not have a taxonomic parent and has at least one child. |
|
231 |
* @return The List<Taxon> of root taxa. |
|
232 |
* @deprecated obsolete when using classification |
|
233 |
*/ |
|
234 |
@Deprecated |
|
235 |
public List<Taxon> getRootTaxa(Reference sec); |
|
236 |
|
|
237 |
|
|
238 |
/** |
|
239 |
* Computes all Taxon instances that do not have a taxonomic parent. |
|
240 |
* @param sec The concept reference that the taxon belongs to |
|
241 |
* @param cdmFetch not used yet !! TODO |
|
242 |
* @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true. |
|
243 |
* @param withMisaplications if false only taxa are returned that have no isMisappliedNameFor relationship. |
|
244 |
* <Br>Default: true. |
|
245 |
* @return The List<Taxon> of root taxa. |
|
246 |
* @deprecated obsolete when using classification |
|
247 |
*/ |
|
248 |
@Deprecated |
|
249 |
public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications); |
|
250 |
|
|
251 |
|
|
252 |
/** |
|
253 |
* Computes all Taxon instances which name is of a certain Rank. |
|
254 |
* |
|
255 |
* @param rank |
|
256 |
* The rank of the taxon name |
|
257 |
* @param sec |
|
258 |
* The concept reference that the taxon belongs to |
|
259 |
* @param cdmFetch |
|
260 |
* not used yet !! TODO |
|
261 |
* @param onlyWithChildren |
|
262 |
* if true only taxa are returned that have taxonomic children. <Br> |
|
263 |
* Default: true. |
|
264 |
* @param withMisaplications |
|
265 |
* if false only taxa are returned that have no |
|
266 |
* isMisappliedNameFor relationship. |
|
267 |
* @param propertyPaths |
|
268 |
* properties to be initialized, For detailed description and |
|
269 |
* examples <b>please refer to:</b> |
|
270 |
* {@link IBeanInitializer#initialize(Object, List)}. <Br> |
|
271 |
* Default: true. |
|
272 |
* @return The List<Taxon> of root taxa. |
|
273 |
* @deprecated obsolete when using classification |
|
274 |
*/ |
|
275 |
@Deprecated |
|
276 |
public List<Taxon> |
|
277 |
getRootTaxa(Rank rank, Reference sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths); |
|
278 |
|
|
279 |
/** |
|
280 |
* TODO necessary? |
|
281 |
* @param pagesize max maximum number of returned taxa |
|
282 |
* @param page page to start, with 0 being first page |
|
283 |
* @return |
|
284 |
*/ |
|
285 |
public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page); |
|
286 |
|
|
287 |
|
|
288 |
/** |
|
289 |
* @param limit |
|
290 |
* @param start |
|
291 |
* @return |
|
292 |
*/ |
|
293 |
public List<Taxon> getAllTaxa(Integer limit, Integer start); |
|
294 |
|
|
295 |
/** |
|
296 |
* @param limit |
|
297 |
* @param start |
|
298 |
* @return |
|
299 |
*/ |
|
300 |
public List<Synonym> getAllSynonyms(Integer limit, Integer start); |
|
301 |
|
|
302 |
public List<RelationshipBase> getAllRelationships(Integer limit, Integer start); |
|
303 |
|
|
304 |
public int countAllRelationships(); |
|
305 |
|
|
306 |
/** |
|
307 |
* @param queryString |
|
308 |
* @param matchMode |
|
309 |
* @param onlyAcccepted |
|
310 |
* @return |
|
311 |
*/ |
|
312 |
public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted); |
|
313 |
|
|
314 |
/** |
|
315 |
* @param queryString |
|
316 |
* @param matchMode |
|
317 |
* @param onlyAcccepted |
|
318 |
* @param criteria |
|
319 |
* @return |
|
320 |
*/ |
|
321 |
public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria); |
|
322 |
|
|
323 |
/** |
|
324 |
* Returns a count of the TaxonRelationships (of where relationship.type == |
|
325 |
* type, if this argument is supplied) where the supplied taxon either is |
|
326 |
* relatedFrom or relatedTo depending on the <code>direction</code> |
|
327 |
* parameter. |
|
328 |
* |
|
329 |
* @param taxon |
|
330 |
* The taxon that is relatedFrom |
|
331 |
* @param type |
|
332 |
* The type of TaxonRelationship (can be null) |
|
333 |
* @param direction |
|
334 |
* specifies the direction of the relationship |
|
335 |
* @return the number of TaxonRelationship instances |
|
336 |
*/ |
|
337 |
public int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type, |
|
338 |
Direction direction); |
|
339 |
|
|
340 |
/** |
|
341 |
* Returns the TaxonRelationships (of where relationship.type == type, if |
|
342 |
* this argument is supplied) where the supplied taxon either is |
|
343 |
* relatedFrom or relatedTo depending on the <code>direction</code> |
|
344 |
* parameter. |
|
345 |
* |
|
346 |
* @param taxon |
|
347 |
* The taxon that is relatedTo |
|
348 |
* @param type |
|
349 |
* The type of TaxonRelationship (can be null) |
|
350 |
* @param pageSize |
|
351 |
* The maximum number of relationships returned (can be null for |
|
352 |
* all relationships) |
|
353 |
* @param pageNumber |
|
354 |
* The offset (in pageSize chunks) from the start of the result |
|
355 |
* set (0 - based) |
|
356 |
* @param orderHints |
|
357 |
* Properties to order by |
|
358 |
* @param propertyPaths |
|
359 |
* Properties to initialize in the returned entities, following |
|
360 |
* the syntax described in |
|
361 |
* {@link IBeanInitializer#initialize(Object, List)} |
|
362 |
* @param direction |
|
363 |
* specifies the direction of the relationship |
|
364 |
* @return a List of TaxonRelationship instances |
|
365 |
*/ |
|
366 |
public List<TaxonRelationship> getTaxonRelationships(Taxon taxon, |
|
367 |
TaxonRelationshipType type, Integer pageSize, Integer pageNumber, |
|
368 |
List<OrderHint> orderHints, List<String> propertyPaths, |
|
369 |
Direction direction); |
|
370 |
|
|
371 |
/** |
|
372 |
* Returns a count of the SynonymRelationships (of where relationship.type == type, |
|
373 |
* if this arguement is supplied) where the supplied taxon is relatedTo. |
|
374 |
* |
|
375 |
* @param taxon The taxon that is relatedTo |
|
376 |
* @param type The type of SynonymRelationship (can be null) |
|
377 |
* @return the number of SynonymRelationship instances |
|
378 |
*/ |
|
379 |
public int countSynonyms(Taxon taxon, SynonymRelationshipType type); |
|
380 |
|
|
381 |
/** |
|
382 |
* Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) |
|
383 |
* where the supplied taxon is relatedTo. |
|
384 |
* |
|
385 |
* @param taxon The taxon that is relatedTo |
|
386 |
* @param type The type of SynonymRelationship (can be null) |
|
387 |
* @param pageSize The maximum number of relationships returned (can be null for all relationships) |
|
388 |
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) |
|
389 |
* * @param orderHints Properties to order by |
|
390 |
* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)} |
|
391 |
* @return a List of SynonymRelationship instances |
|
392 |
*/ |
|
393 |
public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths); |
|
394 |
|
|
395 |
/** |
|
396 |
* Returns a count of the SynonymRelationships (of where relationship.type == type, |
|
397 |
* if this arguement is supplied) where the supplied synonym is relatedFrom. |
|
398 |
* |
|
399 |
* @param taxon The synonym that is relatedFrom |
|
400 |
* @param type The type of SynonymRelationship (can be null) |
|
401 |
* @return the number of SynonymRelationship instances |
|
402 |
*/ |
|
403 |
public int countSynonyms(Synonym synonym, SynonymRelationshipType type); |
|
404 |
|
|
405 |
/** |
|
406 |
* Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied) |
|
407 |
* where the supplied synonym is relatedFrom. |
|
408 |
* |
|
409 |
* @param taxon The synonym that is relatedFrom |
|
410 |
* @param type The type of SynonymRelationship (can be null) |
|
411 |
* @param pageSize The maximum number of relationships returned (can be null for all relationships) |
|
412 |
* @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based) |
|
413 |
* * @param orderHints Properties to order by |
|
414 |
* @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)} |
|
415 |
* @return a List of SynonymRelationship instances |
|
416 |
*/ |
|
417 |
public List<SynonymRelationship> getSynonyms(Synonym synoynm, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths); |
|
418 |
|
|
419 |
|
|
420 |
/** |
|
421 |
* Creates all inferred synonyms for the species in the tree and insert it to the database |
|
422 |
* @param tree |
|
423 |
* @return List of inferred synonyms |
|
424 |
*/ |
|
425 |
//public List<Synonym> insertAllInferredSynonymy(Classification tree); |
|
426 |
|
|
427 |
|
|
428 |
|
|
429 |
public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath); |
|
430 |
public String getPhylumName(TaxonNameBase name); |
|
431 |
|
|
432 |
public long countTaxaByCommonName(String searchString, |
|
433 |
Classification classification, MatchMode matchMode, |
|
434 |
Set<NamedArea> namedAreas); |
|
435 |
|
|
436 |
/** |
|
437 |
* Deletes all synonym relationships of a given synonym. |
|
438 |
* If taxon is given only those relationships to the taxon |
|
439 |
* are deleted. |
|
440 |
* @param synonym the synonym |
|
441 |
* @param taxon the taxon, may be <code>null</code> |
|
442 |
* @return |
|
443 |
* @deprecated This method must no longer being used since the |
|
444 |
* SynonymRelationship is annotated at the {@link Taxon} and at |
|
445 |
* the {@link Synonym} with <code>orphanDelete=true</code>. Just |
|
446 |
* remove the from and to entities from the relationship and |
|
447 |
* hibernate will care for the deletion. Using this method can cause |
|
448 |
* <code>StaleStateException</code> (see http://dev.e-taxonomy.eu/trac/ticket/3797) |
|
449 |
*/ |
|
450 |
@Deprecated |
|
451 |
public long deleteSynonymRelationships(Synonym syn, Taxon taxon); |
|
452 |
|
|
453 |
public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPath); |
|
454 |
|
|
455 |
public List<TaxonNameBase> findIdenticalNamesNew(List <String> propertyPaths); |
|
456 |
|
|
457 |
|
|
458 |
public Integer countSynonymRelationships(TaxonBase taxonBase, |
|
459 |
SynonymRelationshipType type, Direction relatedfrom); |
|
460 |
|
|
461 |
public List<SynonymRelationship> getSynonymRelationships(TaxonBase taxonBase, |
|
462 |
SynonymRelationshipType type, Integer pageSize, Integer pageNumber, |
|
463 |
List<OrderHint> orderHints, List<String> propertyPaths, |
|
464 |
Direction relatedfrom); |
|
465 |
|
|
466 |
/** |
|
467 |
* @return |
|
468 |
*/ |
|
469 |
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon(Integer limit, String pattern); |
|
470 |
|
|
471 |
/** |
|
472 |
* @return |
|
473 |
*/ |
|
474 |
public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym(Integer limit, String pattern); |
|
475 |
|
|
476 |
public List<UuidAndTitleCache<IdentifiableEntity>> getTaxaByNameForEditor(boolean doTaxa, boolean doSynonyms, boolean doNamesWithoutTaxa, boolean doMisappliedNames, String queryString, Classification classification, |
|
477 |
MatchMode matchMode, Set<NamedArea> namedAreas); |
|
478 |
|
|
479 |
public List<String> taxaByNameNotInDB(List<String> taxonNames); |
|
480 |
|
|
481 |
public List<Taxon> listAcceptedTaxaFor(Synonym synonym, Classification classificationFilter, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, |
|
482 |
List<String> propertyPaths); |
|
483 |
|
|
484 |
public long countAcceptedTaxaFor(Synonym synonym, Classification classificationFilter); |
|
485 |
|
|
486 |
public List<UuidAndTitleCache<IdentifiableEntity>> getTaxaByCommonNameForEditor( |
|
487 |
String titleSearchStringSqlized, Classification classification, |
|
488 |
MatchMode matchMode, Set namedAreas); |
|
489 |
|
|
490 |
public <S extends TaxonBase> List<Object[]> findByIdentifier(Class<S> clazz, String identifier, |
|
491 |
DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode, |
|
492 |
boolean includeEntity, Integer pageSize, Integer pageNumber, List<String> propertyPaths); |
|
493 |
|
|
494 |
public <S extends TaxonBase> int countByIdentifier(Class<S> clazz, |
|
495 |
String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter, MatchMode matchmode); |
|
496 |
|
|
497 |
/** |
|
498 |
* @param classification |
|
499 |
* @param excludeUuid |
|
500 |
* @param limit |
|
501 |
* @param pattern |
|
502 |
* @return |
|
503 |
*/ |
|
504 |
List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification( |
|
505 |
Classification classification, List<UUID> excludeUuid, Integer limit, String pattern); |
|
506 |
|
|
507 |
} |
Also available in: Unified diff
Simplify taxonDao