import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
import eu.etaxonomy.cdm.api.service.pager.Pager;
+import eu.etaxonomy.cdm.compare.taxon.TaxonNodeSortMode;
+import eu.etaxonomy.cdm.exception.FilterException;
+import eu.etaxonomy.cdm.exception.UnpublishedException;
import eu.etaxonomy.cdm.model.common.MarkerType;
import eu.etaxonomy.cdm.model.media.MediaRepresentation;
import eu.etaxonomy.cdm.model.name.Rank;
-import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.taxon.Classification;
import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
-import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
+import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
import eu.etaxonomy.cdm.persistence.query.OrderHint;
/**
* @author n.hoffmann
- * @created Sep 21, 2009
+ * @since Sep 21, 2009
*/
public interface IClassificationService extends IIdentifiableEntityService<Classification> {
- /**
- *
- * @param uuid
- * @return
- */
- public TaxonNode getTaxonNodeByUuid(UUID uuid);
-
- /**
- *
- * @param uuid
- * @return
- */
public ITaxonTreeNode getTreeNodeByUuid(UUID uuid);
/**
- *
* Returns the root node of the the given classification (specified by its UUID)
* @param classificationUuid the uuid of the classification
* @return the root node of the classification
public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid);
- /**
- * Clones an existing classification including all taxa and taxon nodes.
- * @param name
- * @param sec
- * @param relationshipType
- * @return
- */
- public UpdateResult cloneClassification(UUID classificationUuid, String name, Reference sec, TaxonRelationshipType relationshipType);
-
- /**
- *
- * @param limit
- * @param start
- * @param orderHints
- * @param propertyPaths
- * @return
- */
public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
/**
public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths);
/**
+ * Loads all TaxonNodes of the specified classification for a given Rank or lower.
+ * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
+ * Rank the according node associated with the next lower Rank is taken as root node in this case.
+ * So the nodes returned may reference Taxa with different Ranks.
*
- * @param taxonNode
+ * If the <code>rank</code> is null the absolute root nodes will be returned.
+
+ * @param classification may be null for all classifications
+ * @param subtree filter on a taxonomic subtree
+ * @param rank the set to null for to get the root nodes of classifications
+ * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
+ * @param pageSize The maximum number of relationships returned (can be null for all relationships)
+ * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param propertyPaths
* @return
- * @deprecated use TaxonNodeService instead
+ * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
+ * @deprecated use according DTO method instead
*/
@Deprecated
- public TaxonNode loadTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
+ public List<TaxonNode> listRankSpecificRootNodes(Classification classification, TaxonNode subtree,
+ Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
+ List<String> propertyPaths);
/**
* Loads all TaxonNodes of the specified classification for a given Rank or lower.
* So the nodes returned may reference Taxa with different Ranks.
*
* If the <code>rank</code> is null the absolute root nodes will be returned.
- *
+
* @param classification may be null for all classifications
+ * @param subtree filter on a taxonomic subtree
* @param rank the set to null for to get the root nodes of classifications
+ * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param propertyPaths
* @return
+ * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
*
*/
- public List<TaxonNode> listRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize, Integer pageIndex, List<String> propertyPaths);
+ public List<TaxonNodeDto> listRankSpecificRootNodeDtos(Classification classification, TaxonNode subtree,
+ Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
+ List<String> propertyPaths);
/**
* If the <code>rank</code> is null the absolute root nodes will be returned.
*
* @param classification may be null for all classifications
+ * @param subtree the taxonomic subtree filter
* @param rank the set to null for to get the root nodes of classifications
+ * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
* @param pageSize The maximum number of relationships returned (can be null for all relationships)
* @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
* @param propertyPaths
* @return
*
+ * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
+ */
+ public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree,
+ Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
+ List<String> propertyPaths);
+ /**
+ * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
+ * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
*/
- public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, Rank rank, Integer pageSize, Integer pageIndex, List<String> propertyPaths);
+ @Deprecated
+ public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification,
+ Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
+ List<String> propertyPaths);
/**
* @param taxonNode
* @param propertyPaths
* the initialization strategy for the returned TaxonNode
* instances.
+ * @param includeUnpublished
+ * if <code>true</code> no {@link UnpublishedException}
+ * is thrown if any of the taxa in the branch are unpublished
* @return the path of nodes from the <b>base node</b> to the node of the
- * specified taxon.
+ * specified taxon.
+ * @throws UnpublishedException
+ * if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown.
*/
- public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, List<String> propertyPaths);
+ public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank, boolean includeUnpublished,
+ List<String> propertyPaths) throws UnpublishedException;
+ public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, boolean includeUnpublished,
+ List<String> propertyPaths) throws UnpublishedException;
/**
* Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
* Nodes of this rank or in case this rank does not exist in the
* current branch the next lower rank is taken as as root node for
* this rank henceforth called the <b>base node</b>.
+ * @param includeUnpublished
+ * if <code>true</code> no {@link UnpublishedException}
+ * is thrown if any of the taxa in the branch are unpublished
* @param propertyPaths
* the initialization strategy for the returned TaxonNode
* instances.
* @return the path of nodes from the <b>base node</b> to the node of the specified
- * taxon.
+ * taxon.
+ * @throws UnpublishedException
+ * if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
*/
- public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification, Rank baseRank, List<String> propertyPaths);
-
-
+ public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
+ TaxonNode subtree, Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
/**
- * @param taxonUuid
- * @param classificationUuid
+ * Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
+ * alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
+ * transaction, would have to initialize the full taxon tree with all nodes of the taxon.
+ * This would be rather slow compared to using this method.
+ * @param taxon
+ * @param classification
+ * the classification to be used
+ * @param baseRank
+ * specifies the root level of the classification, may be null.
+ * Nodes of this rank or in case this rank does not exist in the
+ * current branch the next lower rank is taken as as root node for
+ * this rank henceforth called the <b>base node</b>.
+ * @param includeUnpublished
+ * if <code>true</code> no {@link UnpublishedException}
+ * is thrown if any of the taxa in the branch are unpublished
* @param propertyPaths
- * @return
+ * the initialization strategy for the returned TaxonNode
+ * instances.
+ * @return the path of nodes from the <b>base node</b> to the node of the specified
+ * taxon.
+ * @throws UnpublishedException
+ * if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
*/
- public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize, Integer pageIndex, List<String> propertyPaths);
+ public List<TaxonNodeDto> loadTreeBranchDTOsToTaxon(Taxon taxon, Classification classification,
+ TaxonNode subtree, Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
+
+ public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
+ Rank baseRank,
+ boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
+
+ public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, List<String> propertyPaths);
+
+ public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException;
+
+ public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode comparator) throws FilterException;
/**
* @param taxonNode
@Deprecated
public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
- /**
- *
- * @param classification
- * @return
- */
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification);
- /**
- *
- * @param taxonNode
- * @param propertyPaths
- * @param size
- * @param height
- * @param widthOrDuration
- * @param mimeTypes
- * @return
- */
+ //FIXME seems not to be used anymore
public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(TaxonNode taxonNode, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes);
/**
- *
- * @param taxonNode
- * @return
- * @deprecated use TaxonNodeService instead
- */
- @Deprecated
- public UUID removeTaxonNode(TaxonNode taxonNode);
-
- /**
- *
- * @param taxonNode
- * @return
- * @deprecated use TaxonNodeService instead
- */
- @Deprecated
- public UUID saveTaxonNode(TaxonNode taxonNode);
-
- /**
- *
* @param taxonNodeCollection
* @return
* @deprecated use TaxonNodeService instead
@Deprecated
public Map<UUID, TaxonNode> saveTaxonNodeAll(Collection<TaxonNode> taxonNodeCollection);
- /**
- *
- * @param treeNode
- * @return
- */
-
public UUID removeTreeNode(ITaxonTreeNode treeNode);
- /**
- *
- * @param treeNode
- * @return
- */
public UUID saveTreeNode(ITaxonTreeNode treeNode);
-
public List<TaxonNode> getAllNodes();
public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator);
- /**
- * @param classificationUuid
- * @param excludeTaxa
- * @return
- */
public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid);
- /**
- * @param classificationUuid
- * @param excludeTaxa
- * @param limit
- * @param pattern
- * @return
- */
- List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
UUID classificationUuid, Integer limit, String pattern);
- /**
- * @param classification
- * @param excludeTaxa
- * @param limit
- * @param pattern
- * @return
- */
- List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
Classification classification, Integer limit, String pattern);
- /**
- * @param taxonUuid
- * @param classificationUuid
- * @param pageSize
- * @param pageIndex
- * @param propertyPaths
- * @return
- */
- List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize, Integer pageIndex,
- List<String> propertyPaths);
+ public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
+ Integer pageSize, Integer pageIndex, List<String> propertyPaths);
- /**
- * @param taxonUuid
- * @param classificationUuid
- * @param pageSize
- * @param pageIndex
- * @param propertyPaths
- * @return
- */
- Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, Integer pageSize, Integer pageIndex,
+ public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
List<String> propertyPaths);
- /**
- * @param classification
- * @return
- */
- ClassificationLookupDTO classificationLookup(Classification classification);
+ public ClassificationLookupDTO classificationLookup(Classification classification);
- DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
+ public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
/**
* Returns the higher taxon id for each taxon in taxonUuids.
* The highter taxon is defined by rank where the lowest rank equal or above minRank
* is taken. If maxRank <> null and no taxon exists with minRank <= rank <= maxRank
* no higher taxon is returned for this taxon.
- *
- * @param taxonUuids
- * @param minRank
- * @param maxRank
- * @return
*/
- List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
+ public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
- /**
- * @param taxonUuids
- * @param classificationUuid
- * @param markerType
- * @param value
- * @return
- */
public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> taxonUuids, UUID classificationUuid,
MarkerType markerType, Boolean value);
-
/**
* Returns the most relevant data of a taxon/taxon node, including children, synonyms
* and certain ancestors if required.
- * @param classificationUuid
- * @param taxonUuid
- * @param doSynonyms
- * @param ancestorMarkers
- * @return
*/
public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,
- Boolean doChildren, Boolean doSynonyms, List<UUID> ancestorMarkers,
- NodeSortMode sortMode);
+ Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
+ TaxonNodeSortMode sortMode);
- /**
- * @param classification
- * @return
- */
public UUID saveClassification(Classification classification);
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications);
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ Classification classification, Integer limit, String pattern, boolean searchForClassifications);
+
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ UUID classificationUuid, boolean searchForClassifications);
+
+ public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ Classification classification, boolean searchForClassifications);
+
+ List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
+ UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications,
+ boolean includeDoubtful);
}
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