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      * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 118      * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
 119      */
 120     @Deprecated
 121     public List<TaxonNode> listRankSpecificRootNodes(Classification classification,
 122             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 123             List<String> propertyPaths);
 124
 125
 126     /**
 127      * Loads all TaxonNodes of the specified classification for a given Rank or lower.
 128      * If a branch of the classification tree is not containing a TaxonNode with a Taxon at the given
 129      * Rank the according node associated with the next lower Rank is taken as root node in this case.
 130      * So the nodes returned may reference Taxa with different Ranks.
 131      *
 132      * If the <code>rank</code> is null the absolute root nodes will be returned.
 133      *
 134      * @param classification may be null for all classifications
 135      * @param subtree the taxonomic subtree filter
 136      * @param rank the set to null for to get the root nodes of classifications
 137      * @param includeUnpublished if <code>true</code> unpublished taxa are also exported
 138      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 139      * @param pageIndex The offset (in pageSize chunks) from the start of the result set (0 - based)
 140      * @param propertyPaths
 141      * @return
 142      *
 143      * @see #listRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 144      */
 145     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification, TaxonNode subtree,
 146             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 147             List<String> propertyPaths);
 148     /**
 149      * @see #pageRankSpecificRootNodes(Classification, TaxonNode, Rank, boolean, Integer, Integer, List)
 150      * @deprecated keep this for compatibility to older versions, might be removed in versions >5.3
 151      */
 152     @Deprecated
 153     public Pager<TaxonNode> pageRankSpecificRootNodes(Classification classification,
 154             Rank rank, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 155             List<String> propertyPaths);
 156
 157     /**
 158      * @param taxonNode
 159      * @param baseRank
 160      *            specifies the root level of the classification, may be null.
 161      *            Nodes of this rank or in case this rank does not exist in the
 162      *            current branch the next lower rank is taken as root node for
 163      *            this rank henceforth called the <b>base node</b>.
 164      * @param propertyPaths
 165      *            the initialization strategy for the returned TaxonNode
 166      *            instances.
 167      * @param includeUnpublished
 168      *            if <code>true</code> no {@link UnpublishedException}
 169      *            is thrown if any of the taxa in the branch are unpublished
 170      * @return the path of nodes from the <b>base node</b> to the node of the
 171      *            specified taxon.
 172      * @throws UnpublishedException
 173      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown.
 174      */
 175     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, TaxonNode subtree, Rank baseRank, boolean includeUnpublished,
 176             List<String> propertyPaths) throws UnpublishedException;
 177     public List<TaxonNode> loadTreeBranch(TaxonNode taxonNode, Rank baseRank, boolean includeUnpublished,
 178             List<String> propertyPaths) throws UnpublishedException;
 179
 180     /**
 181      * Although this method seems to be a redundant alternative to {@link #loadChildNodesOfTaxonNode(TaxonNode, List)} it is an important
 182      * alternative from which web services benefit. Without this method the web service controller method, which operates outside of the
 183      * transaction, would have to initialize the full taxon tree with all nodes of the taxon.
 184      * This would be rather slow compared to using this method.
 185      * @param taxon
 186      * @param classification
 187      *            the classification to be used
 188      * @param baseRank
 189      *            specifies the root level of the classification, may be null.
 190      *            Nodes of this rank or in case this rank does not exist in the
 191      *            current branch the next lower rank is taken as as root node for
 192      *            this rank henceforth called the <b>base node</b>.
 193      * @param includeUnpublished
 194      *            if <code>true</code> no {@link UnpublishedException}
 195      *            is thrown if any of the taxa in the branch are unpublished
 196      * @param propertyPaths
 197      *            the initialization strategy for the returned TaxonNode
 198      *            instances.
 199      * @return the path of nodes from the <b>base node</b> to the node of the specified
 200      *            taxon.
 201      * @throws UnpublishedException
 202      *            if any of the taxa in the path is unpublished an {@link UnpublishedException} is thrown
 203      */
 204     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 205             TaxonNode subtree, Rank baseRank,
 206             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 207     public List<TaxonNode> loadTreeBranchToTaxon(Taxon taxon, Classification classification,
 208             Rank baseRank,
 209             boolean includeUnpublished, List<String> propertyPaths) throws UnpublishedException;
 210
 211     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 212             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 213
 214     public List<TaxonNode> listChildNodesOfTaxon(UUID taxonUuid, UUID classificationUuid, UUID subtreeUuid, boolean includeUnpublished,
 215             Integer pageSize, Integer pageIndex, List<String> propertyPaths) throws FilterException;
 216
 217
 218     /**
 219      * @param taxonNode
 220      * @param propertyPaths
 221      * @deprecated move to TaxonNodeService
 222      * @return
 223      */
 224     @Deprecated
 225     public List<TaxonNode> loadChildNodesOfTaxonNode(TaxonNode taxonNode, List<String> propertyPaths);
 226
 227     /**
 228      *
 229      * @param classification
 230      * @return
 231      */
 232     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(Classification classification);
 233
 234     public Map<UUID, List<MediaRepresentation>> getAllMediaForChildNodes(TaxonNode taxonNode, List<String> propertyPaths, int size, int height, int widthOrDuration, String[] mimeTypes);
 235
 236     /**
 237      *
 238      * @param taxonNode
 239      * @return
 240      * @deprecated use TaxonNodeService instead
 241      */
 242     @Deprecated
 243     public UUID removeTaxonNode(TaxonNode taxonNode);
 244
 245     /**
 246      *
 247      * @param taxonNode
 248      * @return
 249      * @deprecated use TaxonNodeService instead
 250      */
 251     @Deprecated
 252     public UUID saveTaxonNode(TaxonNode taxonNode);
 253
 254     /**
 255      *
 256      * @param taxonNodeCollection
 257      * @return
 258      * @deprecated use TaxonNodeService instead
 259      */
 260     @Deprecated
 261     public Map<UUID, TaxonNode> saveTaxonNodeAll(Collection<TaxonNode> taxonNodeCollection);
 262
 263     public UUID removeTreeNode(ITaxonTreeNode treeNode);
 264
 265     public UUID saveTreeNode(ITaxonTreeNode treeNode);
 266
 267     public List<TaxonNode> getAllNodes();
 268
 269         public UpdateResult createHierarchyInClassification(Classification classification, CreateHierarchyForClassificationConfigurator configurator);
 270
 271     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(UUID classificationUuid);
 272
 273     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 274             UUID classificationUuid, Integer limit, String pattern);
 275
 276     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 277             Classification classification, Integer limit, String pattern);
 278
 279     public List<TaxonNode> listSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished,
 280             Integer pageSize, Integer pageIndex, List<String> propertyPaths);
 281
 282     public Pager<TaxonNode> pageSiblingsOfTaxon(UUID taxonUuid, UUID classificationUuid, boolean includeUnpublished, Integer pageSize, Integer pageIndex,
 283             List<String> propertyPaths);
 284
 285     public ClassificationLookupDTO classificationLookup(Classification classification);
 286
 287     public DeleteResult delete(UUID classificationUuid, TaxonDeletionConfigurator config);
 288
 289     /**
 290      * Returns the higher taxon id for each taxon in taxonUuids.
 291      * The highter taxon is defined by rank where the lowest rank equal or above minRank
 292      * is taken. If maxRank <> null and no taxon exists with minRank <= rank <= maxRank
 293      * no higher taxon is returned for this taxon.
 294      *
 295      * @param taxonUuids
 296      * @param minRank
 297      * @param maxRank
 298      * @return
 299      */
 300     public List<GroupedTaxonDTO> groupTaxaByHigherTaxon(List<UUID> taxonUuids, UUID classificationUuid, Rank minRank, Rank maxRank);
 301
 302     /**
 303      * @param taxonUuids
 304      * @param classificationUuid
 305      * @param markerType
 306      * @param value
 307      * @return
 308      */
 309     public List<GroupedTaxonDTO> groupTaxaByMarkedParents(List<UUID> taxonUuids, UUID classificationUuid,
 310             MarkerType markerType, Boolean value);
 311
 312
 313     /**
 314      * Returns the most relevant data of a taxon/taxon node, including children, synonyms
 315      * and certain ancestors if required.
 316      * @param classificationUuid
 317      * @param taxonUuid
 318      * @param doSynonyms
 319      * @param includeUnpublished
 320      * @param ancestorMarkers
 321      * @return
 322      */
 323     public TaxonInContextDTO getTaxonInContext(UUID classificationUuid, UUID taxonUuid,
 324             Boolean doChildren, Boolean doSynonyms, boolean includeUnpublished, List<UUID> ancestorMarkers,
 325             NodeSortMode sortMode);
 326
 327     /**
 328      * @param classification
 329      * @return
 330      */
 331     public UUID saveClassification(Classification classification);
 332
 333     /**
 334      * @param classificationUuid
 335      * @param limit
 336      * @param pattern
 337      * @param searchForClassifications
 338      * @return
 339      */
 340     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 341             UUID classificationUuid, Integer limit, String pattern, boolean searchForClassifications);
 342
 343     /**
 344      * @param classification
 345      * @param limit
 346      * @param pattern
 347      * @param searchForClassifications
 348      * @return
 349      */
 350     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 351             Classification classification, Integer limit, String pattern, boolean searchForClassifications);
 352
 353     /**
 354      * @param classificationUuid
 355      * @param searchForClassifications
 356      * @return
 357      */
 358     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 359             UUID classificationUuid, boolean searchForClassifications);
 360
 361     /**
 362      * @param classification
 363      * @param searchForClassifications
 364      * @return
 365      */
 366     public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(
 367             Classification classification, boolean searchForClassifications);
 368
 369 }