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/**
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* Copyright (C) 2007 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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import java.util.Collection;
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import java.util.List;
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import java.util.Map;
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import java.util.UUID;
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import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;
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import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
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import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
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import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.exception.FilterException;
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import eu.etaxonomy.cdm.exception.UnpublishedException;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.media.MediaRepresentation;
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import eu.etaxonomy.cdm.model.name.Rank;
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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.ITaxonTreeNode;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
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import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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/**
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* @author n.hoffmann
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* @since Sep 21, 2009
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*/
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public interface IClassificationService extends IIdentifiableEntityService<Classification> {
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/**
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*
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* @param uuid
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* @return
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*/
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public ITaxonTreeNode getTreeNodeByUuid(UUID uuid);
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/**
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*
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* Returns the root node of the the given classification (specified by its UUID)
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* @param classificationUuid the uuid of the classification
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* @return the root node of the classification
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*/
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public TaxonNode getRootNode(UUID classificationUuid);
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public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid);
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/**
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* Clones an existing classification including all taxa and taxon nodes.
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* @param name
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* @param sec
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* @param relationshipType
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* @return
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*/
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public UpdateResult cloneClassification(UUID classificationUuid, String name, Reference sec, TaxonRelationshipType relationshipType);
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/**
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*
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* @param limit
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* @param start
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* @param orderHints
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* @param propertyPaths
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* @return
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*/
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public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
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/**
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*
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* @param taxon
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* @param classificationUuid
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* @param propertyPaths
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* @return
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* @deprecated use loadTaxonNode(TaxonNode taxonNode, ...) instead
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* if you have a classification and a taxon that is in it, you should also have the according taxonNode
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*/
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@Deprecated
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public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths);
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/**
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* Loads all TaxonNodes of the specified classification for a given Rank or lower.
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* If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
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* Rank the according node associated with the next lower Rank is taken as root node in this case.
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* So the nodes returned may reference Taxa with different Ranks.
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*
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* If the <code>rank</code> is null the absolute root nodes will be returned.
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* @param classification may be null for all classifications
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* @param subtree filter on a taxonomic subtree
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* @param rank the set to null for to get the root nodes of classifications
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* @param includeUnpublished if <code>true</code> unpublished taxa are also exported
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param propertyPaths
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* @return
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* @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
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* @deprecated use according DTO method instead
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*/
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@Deprecated
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public List<TaxonNode> listRankSpecificRootNodes(Classification classification, TaxonNode subtree,
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Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
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List<String> propertyPaths);
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/**
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* Loads all TaxonNodes of the specified classification for a given Rank or lower.
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* If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
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* Rank the according node associated with the next lower Rank is taken as root node in this case.
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* So the nodes returned may reference Taxa with different Ranks.
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*
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* If the <code>rank</code> is null the absolute root nodes will be returned.
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* @param classification may be null for all classifications
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* @param subtree filter on a taxonomic subtree
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* @param rank the set to null for to get the root nodes of classifications
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* @param includeUnpublished if <code>true</code> unpublished taxa are also exported
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param propertyPaths
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* @return
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* @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
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*
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*/
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public List<TaxonNodeDto> listRankSpecificRootNodeDtos(Classification classification, TaxonNode subtree,
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Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
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List<String> propertyPaths);
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/**
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* Loads all TaxonNodes of the specified classification for a given Rank or lower.
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* If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
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* Rank the according node associated with the next lower Rank is taken as root node in this case.
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* So the nodes returned may reference Taxa with different Ranks.
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*
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* If the <code>rank</code> is null the absolute root nodes will be returned.
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*
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* @param classification may be null for all classifications
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* @param subtree the taxonomic subtree filter
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* @param rank the set to null for to get the root nodes of classifications
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* @param includeUnpublished if <code>true</code> unpublished taxa are also exported
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* @param pageSize The maximum number of relationships returned (can be null for all relationships)
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* @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
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* @param propertyPaths
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* @return
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*
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* @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
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*/
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public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree,
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Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
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List<String> propertyPaths);
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/**
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* @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
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* @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
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*/
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@Deprecated
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public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification,
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Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
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List<String> propertyPaths);
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/**
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* @param taxonNode
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* @param baseRank
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* specifies the root level of the classification, may be null.
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* Nodes of this rank or in case this rank does not exist in the
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* current branch the next lower rank is taken as root node for
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* this rank henceforth called the <b>base node</b>.
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* @param propertyPaths
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* the initialization strategy for the returned TaxonNode
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* instances.
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* @param includeUnpublished
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* if <code>true</code> no {@link UnpublishedException}
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* is thrown if any of the taxa in the branch are unpublished
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* @return the path of nodes from the <b>base node</b> to the node of the
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* specified taxon.
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* @throws UnpublishedException
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* if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown.
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*/
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public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank, boolean includeUnpublished,
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List<String> propertyPaths) throws UnpublishedException;
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public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, boolean includeUnpublished,
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List<String> propertyPaths) throws UnpublishedException;
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/**
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* Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
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* alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
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* transaction, would have to initialize the full taxon tree with all nodes of the taxon.
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* This would be rather slow compared to using this method.
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* @param taxon
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* @param classification
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* the classification to be used
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* @param baseRank
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* specifies the root level of the classification, may be null.
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* Nodes of this rank or in case this rank does not exist in the
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* current branch the next lower rank is taken as as root node for
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* this rank henceforth called the <b>base node</b>.
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* @param includeUnpublished
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* if <code>true</code> no {@link UnpublishedException}
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* is thrown if any of the taxa in the branch are unpublished
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* @param propertyPaths
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* the initialization strategy for the returned TaxonNode
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* instances.
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* @return the path of nodes from the <b>base node</b> to the node of the specified
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* taxon.
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* @throws UnpublishedException
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* if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
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*/
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public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
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TaxonNode subtree, Rank baseRank,
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boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
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/**
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* Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
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* alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
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* transaction, would have to initialize the full taxon tree with all nodes of the taxon.
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* This would be rather slow compared to using this method.
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* @param taxon
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* @param classification
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* the classification to be used
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* @param baseRank
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* specifies the root level of the classification, may be null.
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* Nodes of this rank or in case this rank does not exist in the
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* current branch the next lower rank is taken as as root node for
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* this rank henceforth called the <b>base node</b>.
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* @param includeUnpublished
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* if <code>true</code> no {@link UnpublishedException}
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* is thrown if any of the taxa in the branch are unpublished
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* @param propertyPaths
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* the initialization strategy for the returned TaxonNode
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* instances.
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* @return the path of nodes from the <b>base node</b> to the node of the specified
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* taxon.
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* @throws UnpublishedException
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* if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
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*/
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public List<TaxonNodeDto> loadTreeBranchDTOsToTaxon(Taxon taxon, Classification classification,
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TaxonNode subtree, Rank baseRank,
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boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
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public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
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Rank baseRank,
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boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
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public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
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Integer pageSize, Integer pageIndex, List<String> propertyPaths);
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public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
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Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException;
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public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
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Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode comparator, List<String> propertyPaths) throws FilterException;
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/**
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* @param taxonNode
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* @param propertyPaths
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* @deprecated move to TaxonNodeService
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* @return
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*/
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@Deprecated
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public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
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/**
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*
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* @param classification
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* @return
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*/
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public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification);
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public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(TaxonNode taxonNode, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes);
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/**
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*
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* @param taxonNode
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* @return
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* @deprecated use TaxonNodeService instead
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*/
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@Deprecated
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public UUID removeTaxonNode(TaxonNode taxonNode);
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/**
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*
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* @param taxonNode
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* @return
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* @deprecated use TaxonNodeService instead
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*/
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@Deprecated
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public UUID saveTaxonNode(TaxonNode taxonNode);
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/**
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*
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* @param taxonNodeCollection
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* @return
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* @deprecated use TaxonNodeService instead
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*/
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@Deprecated
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public Map<UUID, TaxonNode> saveTaxonNodeAll(Collection<TaxonNode> taxonNodeCollection);
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public UUID removeTreeNode(ITaxonTreeNode treeNode);
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public UUID saveTreeNode(ITaxonTreeNode treeNode);
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public List<TaxonNode> getAllNodes();
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public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator);
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public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid);
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public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
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UUID classificationUuid, Integer limit, String pattern);
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public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
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Classification classification, Integer limit, String pattern);
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public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
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Integer pageSize, Integer pageIndex, List<String> propertyPaths);
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public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
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List<String> propertyPaths);
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public ClassificationLookupDTO classificationLookup(Classification classification);
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public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
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/**
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* Returns the higher taxon id for each taxon in taxonUuids.
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|
337
|
* The highter taxon is defined by rank where the lowest rank equal or above minRank
|
|
338
|
* is taken. If maxRank <> null and no taxon exists with minRank <= rank <= maxRank
|
|
339
|
* no higher taxon is returned for this taxon.
|
|
340
|
*
|
|
341
|
* @param taxonUuids
|
|
342
|
* @param minRank
|
|
343
|
* @param maxRank
|
|
344
|
* @return
|
|
345
|
*/
|
|
346
|
public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
|
|
347
|
|
|
348
|
/**
|
|
349
|
* @param taxonUuids
|
|
350
|
* @param classificationUuid
|
|
351
|
* @param markerType
|
|
352
|
* @param value
|
|
353
|
* @return
|
|
354
|
*/
|
|
355
|
public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> taxonUuids, UUID classificationUuid,
|
|
356
|
MarkerType markerType, Boolean value);
|
|
357
|
|
|
358
|
|
|
359
|
/**
|
|
360
|
* Returns the most relevant data of a taxon/taxon node, including children, synonyms
|
|
361
|
* and certain ancestors if required.
|
|
362
|
* @param classificationUuid
|
|
363
|
* @param taxonUuid
|
|
364
|
* @param doSynonyms
|
|
365
|
* @param includeUnpublished
|
|
366
|
* @param ancestorMarkers
|
|
367
|
* @return
|
|
368
|
*/
|
|
369
|
public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,
|
|
370
|
Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
|
|
371
|
TaxonNodeSortMode sortMode);
|
|
372
|
|
|
373
|
/**
|
|
374
|
* @param classification
|
|
375
|
* @return
|
|
376
|
*/
|
|
377
|
public UUID saveClassification(Classification classification);
|
|
378
|
|
|
379
|
/**
|
|
380
|
* @param classificationUuid
|
|
381
|
* @param limit
|
|
382
|
* @param pattern
|
|
383
|
* @param searchForClassifications
|
|
384
|
* @return
|
|
385
|
*/
|
|
386
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
|
387
|
UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications);
|
|
388
|
|
|
389
|
/**
|
|
390
|
* @param classification
|
|
391
|
* @param limit
|
|
392
|
* @param pattern
|
|
393
|
* @param searchForClassifications
|
|
394
|
* @return
|
|
395
|
*/
|
|
396
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
|
397
|
Classification classification, Integer limit, String pattern, boolean searchForClassifications);
|
|
398
|
|
|
399
|
/**
|
|
400
|
* @param classificationUuid
|
|
401
|
* @param searchForClassifications
|
|
402
|
* @return
|
|
403
|
*/
|
|
404
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
|
405
|
UUID classificationUuid, boolean searchForClassifications);
|
|
406
|
|
|
407
|
/**
|
|
408
|
* @param classification
|
|
409
|
* @param searchForClassifications
|
|
410
|
* @return
|
|
411
|
*/
|
|
412
|
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
|
|
413
|
Classification classification, boolean searchForClassifications);
|
|
414
|
|
|
415
|
}
|