cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/IClassificationService.java

   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.api.service;
  11
  12 import java.util.Collection;
  13 import java.util.List;
  14 import java.util.Map;
  15 import java.util.UUID;
  16
  17 import eu.etaxonomy.cdm.api.service.config.CreateHierarchyForClassificationConfigurator;
  18 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  19 import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
  20 import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
  21 import eu.etaxonomy.cdm.api.service.pager.Pager;
  22 import eu.etaxonomy.cdm.exception.FilterException;
  23 import eu.etaxonomy.cdm.exception.UnpublishedException;
  24 import eu.etaxonomy.cdm.model.common.MarkerType;
  25 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  26 import eu.etaxonomy.cdm.model.name.Rank;
  27 import eu.etaxonomy.cdm.model.reference.Reference;
  28 import eu.etaxonomy.cdm.model.taxon.Classification;
  29 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  30 import eu.etaxonomy.cdm.model.taxon.Taxon;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  33 import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
  34 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  35 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  36
  37
  38 /**
  39  * @author n.hoffmann
  40  * @since Sep 21, 2009
  41  */
  42 public interface IClassificationService extends IIdentifiableEntityService<Classification> {
  43
  44     /**
  45      *
  46      * @param uuid
  47      * @return
  48      */
  49     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid);
  50
  51     /**
  52      *
  53      * Returns the root node of the the given classification (specified by its UUID)
  54      * @param classificationUuid the uuid of the classification
  55      * @return the root node of the classification
  56      */
  57     public TaxonNode getRootNode(UUID classificationUuid);
  58
  59     public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid);
  60
  61     /**
  62      * Clones an existing classification including all taxa and taxon nodes.
  63      * @param name
  64      * @param sec
  65      * @param relationshipType
  66      * @return
  67      */
  68     public UpdateResult cloneClassification(UUID classificationUuid, String name, Reference sec, TaxonRelationshipType relationshipType);
  69
  70     /**
  71      *
  72      * @param limit
  73      * @param start
  74      * @param orderHints
  75      * @param propertyPaths
  76      * @return
  77      */
  78     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
  79
  80     /**
  81      *
  82      * @param taxon
  83      * @param classificationUuid
  84      * @param propertyPaths
  85      * @return
  86      * @deprecated use loadTaxonNode(TaxonNode taxonNode, ...) instead
  87      * if you have a classification and a taxon that is in it, you should also have the according taxonNode
  88      */
  89     @Deprecated
  90     public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths);
  91
  92     /**
  93      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
  94      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
  95      * Rank the according node associated with the next lower Rank is taken as root node in this case.
  96      * So the nodes returned may reference Taxa with different Ranks.
  97      *
  98      * If the <code>rank</code> is null the absolute root nodes will be returned.
  99
 100      * @param classification may be null for all classifications
 101      * @param subtree filter on a taxonomic subtree
 102      * @param rank the set to null for to get the root nodes of classifications
 103      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 104      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 105      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 106      * @param propertyPaths
 107      * @return
 108      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 109      *
 110      */
 111     public List<TaxonNode> listRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 112             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 113             List<String> propertyPaths);
 114
 115
 116     /**
 117      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
 118      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
 119      * Rank the according node associated with the next lower Rank is taken as root node in this case.
 120      * So the nodes returned may reference Taxa with different Ranks.
 121      *
 122      * If the <code>rank</code> is null the absolute root nodes will be returned.
 123      *
 124      * @param classification may be null for all classifications
 125      * @param subtree the taxonomic subtree filter
 126      * @param rank the set to null for to get the root nodes of classifications
 127      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 128      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 129      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 130      * @param propertyPaths
 131      * @return
 132      *
 133      * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 134      */
 135     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 136             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 137             List<String> propertyPaths);
 138     /**
 139      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 140      * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
 141      */
 142     @Deprecated
 143     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification,
 144             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 145             List<String> propertyPaths);
 146
 147     /**
 148      * @param taxonNode
 149      * @param baseRank
 150      *            specifies the root level of the classification, may be null.
 151      *            Nodes of this rank or in case this rank does not exist in the
 152      *            current branch the next lower rank is taken as root node for
 153      *            this rank henceforth called the <b>base node</b>.
 154      * @param propertyPaths
 155      *            the initialization strategy for the returned TaxonNode
 156      *            instances.
 157      * @param includeUnpublished
 158      *            if <code>true</code> no {@link UnpublishedException}
 159      *            is thrown if any of the taxa in the branch are unpublished
 160      * @return the path of nodes from the <b>base node</b> to the node of the
 161      *            specified taxon.
 162      * @throws UnpublishedException
 163      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown.
 164      */
 165     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank, boolean includeUnpublished,
 166             List<String> propertyPaths) throws UnpublishedException;
 167     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, boolean includeUnpublished,
 168             List<String> propertyPaths) throws UnpublishedException;
 169
 170     /**
 171      * Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
 172      * alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
 173      * transaction, would have to initialize the full taxon tree with all nodes of the taxon.
 174      * This would be rather slow compared to using this method.
 175      * @param taxon
 176      * @param classification
 177      *            the classification to be used
 178      * @param baseRank
 179      *            specifies the root level of the classification, may be null.
 180      *            Nodes of this rank or in case this rank does not exist in the
 181      *            current branch the next lower rank is taken as as root node for
 182      *            this rank henceforth called the <b>base node</b>.
 183      * @param includeUnpublished
 184      *            if <code>true</code> no {@link UnpublishedException}
 185      *            is thrown if any of the taxa in the branch are unpublished
 186      * @param propertyPaths
 187      *            the initialization strategy for the returned TaxonNode
 188      *            instances.
 189      * @return the path of nodes from the <b>base node</b> to the node of the specified
 190      *            taxon.
 191      * @throws UnpublishedException
 192      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
 193      */
 194     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 195             TaxonNode subtree, Rank baseRank,
 196             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 197     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 198             Rank baseRank,
 199             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 200
 201     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 202             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 203
 204     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 205             Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException;
 206
 207
 208     /**
 209      * @param taxonNode
 210      * @param propertyPaths
 211      * @deprecated move to TaxonNodeService
 212      * @return
 213      */
 214     @Deprecated
 215     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
 216
 217     /**
 218      *
 219      * @param classification
 220      * @return
 221      */
 222     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification);
 223
 224     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(TaxonNode taxonNode, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes);
 225
 226     /**
 227      *
 228      * @param taxonNode
 229      * @return
 230      * @deprecated use TaxonNodeService instead
 231      */
 232     @Deprecated
 233     public UUID removeTaxonNode(TaxonNode taxonNode);
 234
 235     /**
 236      *
 237      * @param taxonNode
 238      * @return
 239      * @deprecated use TaxonNodeService instead
 240      */
 241     @Deprecated
 242     public UUID saveTaxonNode(TaxonNode taxonNode);
 243
 244     /**
 245      *
 246      * @param taxonNodeCollection
 247      * @return
 248      * @deprecated use TaxonNodeService instead
 249      */
 250     @Deprecated
 251     public Map<UUID, TaxonNode> saveTaxonNodeAll(Collection<TaxonNode> taxonNodeCollection);
 252
 253     public UUID removeTreeNode(ITaxonTreeNode treeNode);
 254
 255     public UUID saveTreeNode(ITaxonTreeNode treeNode);
 256
 257     public List<TaxonNode> getAllNodes();
 258
 259         public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator);
 260
 261     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid);
 262
 263     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 264             UUID classificationUuid, Integer limit, String pattern);
 265
 266     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 267             Classification classification, Integer limit, String pattern);
 268
 269     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 270             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 271
 272     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 273             List<String> propertyPaths);
 274
 275     public ClassificationLookupDTO classificationLookup(Classification classification);
 276
 277     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
 278
 279     /**
 280      * Returns the higher taxon id for each taxon in taxonUuids.
 281      * The highter taxon is defined by rank where the lowest rank equal or above minRank
 282      * is taken. If maxRank <> null and no taxon exists with minRank <= rank <= maxRank
 283      * no higher taxon is returned for this taxon.
 284      *
 285      * @param taxonUuids
 286      * @param minRank
 287      * @param maxRank
 288      * @return
 289      */
 290     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
 291
 292     /**
 293      * @param taxonUuids
 294      * @param classificationUuid
 295      * @param markerType
 296      * @param value
 297      * @return
 298      */
 299     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> taxonUuids, UUID classificationUuid,
 300             MarkerType markerType, Boolean value);
 301
 302
 303     /**
 304      * Returns the most relevant data of a taxon/taxon node, including children, synonyms
 305      * and certain ancestors if required.
 306      * @param classificationUuid
 307      * @param taxonUuid
 308      * @param doSynonyms
 309      * @param includeUnpublished
 310      * @param ancestorMarkers
 311      * @return
 312      */
 313     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,
 314             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 315             NodeSortMode sortMode);
 316
 317     /**
 318      * @param classification
 319      * @return
 320      */
 321     public UUID saveClassification(Classification classification);
 322
 323     /**
 324      * @param classificationUuid
 325      * @param limit
 326      * @param pattern
 327      * @param searchForClassifications
 328      * @return
 329      */
 330     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 331             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications);
 332
 333     /**
 334      * @param classification
 335      * @param limit
 336      * @param pattern
 337      * @param searchForClassifications
 338      * @return
 339      */
 340     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 341             Classification classification, Integer limit, String pattern, boolean searchForClassifications);
 342
 343     /**
 344      * @param classificationUuid
 345      * @param searchForClassifications
 346      * @return
 347      */
 348     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 349             UUID classificationUuid, boolean searchForClassifications);
 350
 351     /**
 352      * @param classification
 353      * @param searchForClassifications
 354      * @return
 355      */
 356     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 357             Classification classification, boolean searchForClassifications);
 358
 359 }