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.UnpublishedException;
  23 import eu.etaxonomy.cdm.model.common.MarkerType;
  24 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  25 import eu.etaxonomy.cdm.model.name.Rank;
  26 import eu.etaxonomy.cdm.model.reference.Reference;
  27 import eu.etaxonomy.cdm.model.taxon.Classification;
  28 import eu.etaxonomy.cdm.model.taxon.ITaxonTreeNode;
  29 import eu.etaxonomy.cdm.model.taxon.Taxon;
  30 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  32 import eu.etaxonomy.cdm.persistence.dto.ClassificationLookupDTO;
  33 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  34 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  35
  36
  37 /**
  38  * @author n.hoffmann
  39  * @since Sep 21, 2009
  40  */
  41 public interface IClassificationService extends IIdentifiableEntityService<Classification> {
  42
  43     /**
  44      *
  45      * @param uuid
  46      * @return
  47      */
  48     public ITaxonTreeNode getTreeNodeByUuid(UUID uuid);
  49
  50     /**
  51      *
  52      * Returns the root node of the the given classification (specified by its UUID)
  53      * @param classificationUuid the uuid of the classification
  54      * @return the root node of the classification
  55      */
  56     public TaxonNode getRootNode(UUID classificationUuid);
  57
  58     public UUID getTaxonNodeUuidByTaxonUuid(UUID classificationUuid, UUID taxonUuid);
  59
  60     /**
  61      * Clones an existing classification including all taxa and taxon nodes.
  62      * @param name
  63      * @param sec
  64      * @param relationshipType
  65      * @return
  66      */
  67     public UpdateResult cloneClassification(UUID classificationUuid, String name, Reference sec, TaxonRelationshipType relationshipType);
  68
  69     /**
  70      *
  71      * @param limit
  72      * @param start
  73      * @param orderHints
  74      * @param propertyPaths
  75      * @return
  76      */
  77     public List<Classification> listClassifications(Integer limit, Integer start, List<OrderHint> orderHints, List<String> propertyPaths);
  78
  79     /**
  80      *
  81      * @param taxon
  82      * @param classificationUuid
  83      * @param propertyPaths
  84      * @return
  85      * @deprecated use loadTaxonNode(TaxonNode taxonNode, ...) instead
  86      * if you have a classification and a taxon that is in it, you should also have the according taxonNode
  87      */
  88     @Deprecated
  89     public TaxonNode loadTaxonNodeByTaxon(Taxon taxon, UUID classificationUuid, List<String> propertyPaths);
  90
  91     /**
  92      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
  93      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
  94      * Rank the according node associated with the next lower Rank is taken as root node in this case.
  95      * So the nodes returned may reference Taxa with different Ranks.
  96      *
  97      * If the <code>rank</code> is null the absolute root nodes will be returned.
  98
  99      * @param classification may be null for all classifications
 100      * @param subtree filter on a taxonomic subtree
 101      * @param rank the set to null for to get the root nodes of classifications
 102      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 103      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 104      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 105      * @param propertyPaths
 106      * @return
 107      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 108      *
 109      */
 110     public List<TaxonNode> listRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 111             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 112             List<String> propertyPaths);
 113
 114
 115     /**
 116      * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 117      * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
 118      */
 119     @Deprecated
 120     public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
 121             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 122             List<String> propertyPaths);
 123
 124
 125     /**
 126      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
 127      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
 128      * Rank the according node associated with the next lower Rank is taken as root node in this case.
 129      * So the nodes returned may reference Taxa with different Ranks.
 130      *
 131      * If the <code>rank</code> is null the absolute root nodes will be returned.
 132      *
 133      * @param classification may be null for all classifications
 134      * @param subtree the taxonomic subtree filter
 135      * @param rank the set to null for to get the root nodes of classifications
 136      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 137      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 138      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 139      * @param propertyPaths
 140      * @return
 141      *
 142      * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 143      */
 144     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 145             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 146             List<String> propertyPaths);
 147     /**
 148      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 149      * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
 150      */
 151     @Deprecated
 152     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification,
 153             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 154             List<String> propertyPaths);
 155
 156     /**
 157      * @param taxonNode
 158      * @param baseRank
 159      *            specifies the root level of the classification, may be null.
 160      *            Nodes of this rank or in case this rank does not exist in the
 161      *            current branch the next lower rank is taken as root node for
 162      *            this rank henceforth called the <b>base node</b>.
 163      * @param propertyPaths
 164      *            the initialization strategy for the returned TaxonNode
 165      *            instances.
 166      * @param includeUnpublished
 167      *            if <code>true</code> no {@link UnpublishedException}
 168      *            is thrown if any of the taxa in the branch are unpublished
 169      * @return the path of nodes from the <b>base node</b> to the node of the
 170      *            specified taxon.
 171      * @throws UnpublishedException
 172      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown.
 173      */
 174     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank, boolean includeUnpublished,
 175             List<String> propertyPaths) throws UnpublishedException;
 176     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, boolean includeUnpublished,
 177             List<String> propertyPaths) throws UnpublishedException;
 178
 179     /**
 180      * Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
 181      * alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
 182      * transaction, would have to initialize the full taxon tree with all nodes of the taxon.
 183      * This would be rather slow compared to using this method.
 184      * @param taxon
 185      * @param classification
 186      *            the classification to be used
 187      * @param baseRank
 188      *            specifies the root level of the classification, may be null.
 189      *            Nodes of this rank or in case this rank does not exist in the
 190      *            current branch the next lower rank is taken as as root node for
 191      *            this rank henceforth called the <b>base node</b>.
 192      * @param includeUnpublished
 193      *            if <code>true</code> no {@link UnpublishedException}
 194      *            is thrown if any of the taxa in the branch are unpublished
 195      * @param propertyPaths
 196      *            the initialization strategy for the returned TaxonNode
 197      *            instances.
 198      * @return the path of nodes from the <b>base node</b> to the node of the specified
 199      *            taxon.
 200      * @throws UnpublishedException
 201      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
 202      */
 203     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 204             TaxonNode subtree, Rank baseRank,
 205             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 206     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 207             Rank baseRank,
 208             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 209
 210     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 211             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 212     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 213             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 214
 215
 216     /**
 217      * @param taxonNode
 218      * @param propertyPaths
 219      * @deprecated move to TaxonNodeService
 220      * @return
 221      */
 222     @Deprecated
 223     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
 224
 225     /**
 226      *
 227      * @param classification
 228      * @return
 229      */
 230     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification);
 231
 232     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(TaxonNode taxonNode, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes);
 233
 234     /**
 235      *
 236      * @param taxonNode
 237      * @return
 238      * @deprecated use TaxonNodeService instead
 239      */
 240     @Deprecated
 241     public UUID removeTaxonNode(TaxonNode taxonNode);
 242
 243     /**
 244      *
 245      * @param taxonNode
 246      * @return
 247      * @deprecated use TaxonNodeService instead
 248      */
 249     @Deprecated
 250     public UUID saveTaxonNode(TaxonNode taxonNode);
 251
 252     /**
 253      *
 254      * @param taxonNodeCollection
 255      * @return
 256      * @deprecated use TaxonNodeService instead
 257      */
 258     @Deprecated
 259     public Map<UUID, TaxonNode> saveTaxonNodeAll(Collection<TaxonNode> taxonNodeCollection);
 260
 261     public UUID removeTreeNode(ITaxonTreeNode treeNode);
 262
 263     public UUID saveTreeNode(ITaxonTreeNode treeNode);
 264
 265     public List<TaxonNode> getAllNodes();
 266
 267         public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator);
 268
 269     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid);
 270
 271     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 272             UUID classificationUuid, Integer limit, String pattern);
 273
 274     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 275             Classification classification, Integer limit, String pattern);
 276
 277     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 278             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 279
 280     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 281             List<String> propertyPaths);
 282
 283     public ClassificationLookupDTO classificationLookup(Classification classification);
 284
 285     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
 286
 287     /**
 288      * Returns the higher taxon id for each taxon in taxonUuids.
 289      * The highter taxon is defined by rank where the lowest rank equal or above minRank
 290      * is taken. If maxRank <> null and no taxon exists with minRank <= rank <= maxRank
 291      * no higher taxon is returned for this taxon.
 292      *
 293      * @param taxonUuids
 294      * @param minRank
 295      * @param maxRank
 296      * @return
 297      */
 298     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
 299
 300     /**
 301      * @param taxonUuids
 302      * @param classificationUuid
 303      * @param markerType
 304      * @param value
 305      * @return
 306      */
 307     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> taxonUuids, UUID classificationUuid,
 308             MarkerType markerType, Boolean value);
 309
 310
 311     /**
 312      * Returns the most relevant data of a taxon/taxon node, including children, synonyms
 313      * and certain ancestors if required.
 314      * @param classificationUuid
 315      * @param taxonUuid
 316      * @param doSynonyms
 317      * @param includeUnpublished
 318      * @param ancestorMarkers
 319      * @return
 320      */
 321     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,
 322             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 323             NodeSortMode sortMode);
 324
 325     /**
 326      * @param classification
 327      * @return
 328      */
 329     public UUID saveClassification(Classification classification);
 330
 331     /**
 332      * @param classificationUuid
 333      * @param limit
 334      * @param pattern
 335      * @param searchForClassifications
 336      * @return
 337      */
 338     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 339             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications);
 340
 341     /**
 342      * @param classification
 343      * @param limit
 344      * @param pattern
 345      * @param searchForClassifications
 346      * @return
 347      */
 348     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 349             Classification classification, Integer limit, String pattern, boolean searchForClassifications);
 350
 351     /**
 352      * @param classificationUuid
 353      * @param searchForClassifications
 354      * @return
 355      */
 356     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 357             UUID classificationUuid, boolean searchForClassifications);
 358
 359     /**
 360      * @param classification
 361      * @param searchForClassifications
 362      * @return
 363      */
 364     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 365             Classification classification, boolean searchForClassifications);
 366
 367 }