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.SubtreeCloneConfigurator;
  19 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  20 import eu.etaxonomy.cdm.api.service.dto.GroupedTaxonDTO;
  21 import eu.etaxonomy.cdm.api.service.dto.TaxonInContextDTO;
  22 import eu.etaxonomy.cdm.api.service.pager.Pager;
  23 import eu.etaxonomy.cdm.exception.FilterException;
  24 import eu.etaxonomy.cdm.exception.UnpublishedException;
  25 import eu.etaxonomy.cdm.model.common.MarkerType;
  26 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  27 import eu.etaxonomy.cdm.model.name.Rank;
  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.persistence.dto.ClassificationLookupDTO;
  33 import eu.etaxonomy.cdm.persistence.dto.TaxonNodeDto;
  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     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid);
  45
  46     /**
  47      * Returns the root node of the the given classification (specified by its UUID)
  48      * @param classificationUuid the uuid of the classification
  49      * @return the root node of the classification
  50      */
  51     public TaxonNode getRootNode(UUID classificationUuid);
  52
  53     public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid);
  54
  55     /**
  56      * Clones an existing classification including all taxa and taxon nodes.
  57
  58      * @param config the configurator for the cloning
  59      */
  60     public UpdateResult cloneClassification(SubtreeCloneConfigurator config);
  61
  62     /**
  63      *
  64      * @param limit
  65      * @param start
  66      * @param orderHints
  67      * @param propertyPaths
  68      * @return
  69      */
  70     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
  71
  72     /**
  73      *
  74      * @param taxon
  75      * @param classificationUuid
  76      * @param propertyPaths
  77      * @return
  78      * @deprecated use loadTaxonNode(TaxonNode taxonNode, ...) instead
  79      * if you have a classification and a taxon that is in it, you should also have the according taxonNode
  80      */
  81     @Deprecated
  82     public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths);
  83
  84     /**
  85      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
  86      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
  87      * Rank the according node associated with the next lower Rank is taken as root node in this case.
  88      * So the nodes returned may reference Taxa with different Ranks.
  89      *
  90      * If the <code>rank</code> is null the absolute root nodes will be returned.
  91
  92      * @param classification may be null for all classifications
  93      * @param subtree filter on a taxonomic subtree
  94      * @param rank the set to null for to get the root nodes of classifications
  95      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
  96      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
  97      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
  98      * @param propertyPaths
  99      * @return
 100      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 101      * @deprecated use according DTO method instead
 102      */
 103     @Deprecated
 104     public List<TaxonNode> listRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 105             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 106             List<String> propertyPaths);
 107
 108     /**
 109      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
 110      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
 111      * Rank the according node associated with the next lower Rank is taken as root node in this case.
 112      * So the nodes returned may reference Taxa with different Ranks.
 113      *
 114      * If the <code>rank</code> is null the absolute root nodes will be returned.
 115
 116      * @param classification may be null for all classifications
 117      * @param subtree filter on a taxonomic subtree
 118      * @param rank the set to null for to get the root nodes of classifications
 119      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 120      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 121      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 122      * @param propertyPaths
 123      * @return
 124      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 125      *
 126      */
 127     public List<TaxonNodeDto> listRankSpecificRootNodeDtos(Classification classification, TaxonNode subtree,
 128             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode sortMode,
 129             List<String> propertyPaths);
 130
 131
 132     /**
 133      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
 134      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
 135      * Rank the according node associated with the next lower Rank is taken as root node in this case.
 136      * So the nodes returned may reference Taxa with different Ranks.
 137      *
 138      * If the <code>rank</code> is null the absolute root nodes will be returned.
 139      *
 140      * @param classification may be null for all classifications
 141      * @param subtree the taxonomic subtree filter
 142      * @param rank the set to null for to get the root nodes of classifications
 143      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 144      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 145      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 146      * @param propertyPaths
 147      * @return
 148      *
 149      * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 150      */
 151     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 152             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 153             List<String> propertyPaths);
 154     /**
 155      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 156      * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
 157      */
 158     @Deprecated
 159     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification,
 160             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 161             List<String> propertyPaths);
 162
 163     /**
 164      * @param taxonNode
 165      * @param baseRank
 166      *            specifies the root level of the classification, may be null.
 167      *            Nodes of this rank or in case this rank does not exist in the
 168      *            current branch the next lower rank is taken as root node for
 169      *            this rank henceforth called the <b>base node</b>.
 170      * @param propertyPaths
 171      *            the initialization strategy for the returned TaxonNode
 172      *            instances.
 173      * @param includeUnpublished
 174      *            if <code>true</code> no {@link UnpublishedException}
 175      *            is thrown if any of the taxa in the branch are unpublished
 176      * @return the path of nodes from the <b>base node</b> to the node of the
 177      *            specified taxon.
 178      * @throws UnpublishedException
 179      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown.
 180      */
 181     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank, boolean includeUnpublished,
 182             List<String> propertyPaths) throws UnpublishedException;
 183     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, boolean includeUnpublished,
 184             List<String> propertyPaths) throws UnpublishedException;
 185
 186     /**
 187      * Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
 188      * alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
 189      * transaction, would have to initialize the full taxon tree with all nodes of the taxon.
 190      * This would be rather slow compared to using this method.
 191      * @param taxon
 192      * @param classification
 193      *            the classification to be used
 194      * @param baseRank
 195      *            specifies the root level of the classification, may be null.
 196      *            Nodes of this rank or in case this rank does not exist in the
 197      *            current branch the next lower rank is taken as as root node for
 198      *            this rank henceforth called the <b>base node</b>.
 199      * @param includeUnpublished
 200      *            if <code>true</code> no {@link UnpublishedException}
 201      *            is thrown if any of the taxa in the branch are unpublished
 202      * @param propertyPaths
 203      *            the initialization strategy for the returned TaxonNode
 204      *            instances.
 205      * @return the path of nodes from the <b>base node</b> to the node of the specified
 206      *            taxon.
 207      * @throws UnpublishedException
 208      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
 209      */
 210     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 211             TaxonNode subtree, Rank baseRank,
 212             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 213
 214     /**
 215      * Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
 216      * alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
 217      * transaction, would have to initialize the full taxon tree with all nodes of the taxon.
 218      * This would be rather slow compared to using this method.
 219      * @param taxon
 220      * @param classification
 221      *            the classification to be used
 222      * @param baseRank
 223      *            specifies the root level of the classification, may be null.
 224      *            Nodes of this rank or in case this rank does not exist in the
 225      *            current branch the next lower rank is taken as as root node for
 226      *            this rank henceforth called the <b>base node</b>.
 227      * @param includeUnpublished
 228      *            if <code>true</code> no {@link UnpublishedException}
 229      *            is thrown if any of the taxa in the branch are unpublished
 230      * @param propertyPaths
 231      *            the initialization strategy for the returned TaxonNode
 232      *            instances.
 233      * @return the path of nodes from the <b>base node</b> to the node of the specified
 234      *            taxon.
 235      * @throws UnpublishedException
 236      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
 237      */
 238     public List<TaxonNodeDto> loadTreeBranchDTOsToTaxon(Taxon taxon, Classification classification,
 239             TaxonNode subtree, Rank baseRank,
 240             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 241
 242     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 243             Rank baseRank,
 244             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 245
 246     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 247             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 248
 249     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 250             Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException;
 251
 252     public List<TaxonNodeDto> listChildNodeDtosOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 253             Integer pageSize, Integer pageIndex, TaxonNodeDtoSortMode comparator, List<String> propertyPaths) throws FilterException;
 254
 255     /**
 256      * @param taxonNode
 257      * @param propertyPaths
 258      * @deprecated move to TaxonNodeService
 259      * @return
 260      */
 261     @Deprecated
 262     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
 263
 264     /**
 265      *
 266      * @param classification
 267      * @return
 268      */
 269     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification);
 270
 271     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(TaxonNode taxonNode, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes);
 272
 273     /**
 274      *
 275      * @param taxonNode
 276      * @return
 277      * @deprecated use TaxonNodeService instead
 278      */
 279     @Deprecated
 280     public UUID removeTaxonNode(TaxonNode taxonNode);
 281
 282     /**
 283      *
 284      * @param taxonNode
 285      * @return
 286      * @deprecated use TaxonNodeService instead
 287      */
 288     @Deprecated
 289     public UUID saveTaxonNode(TaxonNode taxonNode);
 290
 291     /**
 292      *
 293      * @param taxonNodeCollection
 294      * @return
 295      * @deprecated use TaxonNodeService instead
 296      */
 297     @Deprecated
 298     public Map<UUID, TaxonNode> saveTaxonNodeAll(Collection<TaxonNode> taxonNodeCollection);
 299
 300     public UUID removeTreeNode(ITaxonTreeNode treeNode);
 301
 302     public UUID saveTreeNode(ITaxonTreeNode treeNode);
 303
 304     public List<TaxonNode> getAllNodes();
 305
 306         public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator);
 307
 308     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid);
 309
 310     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 311             UUID classificationUuid, Integer limit, String pattern);
 312
 313     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 314             Classification classification, Integer limit, String pattern);
 315
 316     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 317             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 318
 319     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 320             List<String> propertyPaths);
 321
 322     public ClassificationLookupDTO classificationLookup(Classification classification);
 323
 324     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
 325
 326     /**
 327      * Returns the higher taxon id for each taxon in taxonUuids.
 328      * The highter taxon is defined by rank where the lowest rank equal or above minRank
 329      * is taken. If maxRank <> null and no taxon exists with minRank <= rank <= maxRank
 330      * no higher taxon is returned for this taxon.
 331      *
 332      * @param taxonUuids
 333      * @param minRank
 334      * @param maxRank
 335      * @return
 336      */
 337     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
 338
 339     /**
 340      * @param taxonUuids
 341      * @param classificationUuid
 342      * @param markerType
 343      * @param value
 344      * @return
 345      */
 346     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> taxonUuids, UUID classificationUuid,
 347             MarkerType markerType, Boolean value);
 348
 349
 350     /**
 351      * Returns the most relevant data of a taxon/taxon node, including children, synonyms
 352      * and certain ancestors if required.
 353      * @param classificationUuid
 354      * @param taxonUuid
 355      * @param doSynonyms
 356      * @param includeUnpublished
 357      * @param ancestorMarkers
 358      * @return
 359      */
 360     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,
 361             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 362             TaxonNodeSortMode sortMode);
 363
 364     /**
 365      * @param classification
 366      * @return
 367      */
 368     public UUID saveClassification(Classification classification);
 369
 370     /**
 371      * @param classificationUuid
 372      * @param limit
 373      * @param pattern
 374      * @param searchForClassifications
 375      * @return
 376      */
 377     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 378             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications);
 379
 380     /**
 381      * @param classification
 382      * @param limit
 383      * @param pattern
 384      * @param searchForClassifications
 385      * @return
 386      */
 387     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 388             Classification classification, Integer limit, String pattern, boolean searchForClassifications);
 389
 390     /**
 391      * @param classificationUuid
 392      * @param searchForClassifications
 393      * @return
 394      */
 395     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 396             UUID classificationUuid, boolean searchForClassifications);
 397
 398     /**
 399      * @param classification
 400      * @param searchForClassifications
 401      * @return
 402      */
 403     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 404             Classification classification, boolean searchForClassifications);
 405
 406     /**
 407      * @param classificationUuid
 408      * @param limit
 409      * @param pattern
 410      * @param searchForClassifications
 411      * @param includeDoubtful
 412      * @return
 413      */
 414     List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 415             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications,
 416             boolean includeDoubtful);
 417
 418 }