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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.util.List;
  14 import java.util.Set;
  15 import java.util.UUID;
  16
  17 import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
  18 import eu.etaxonomy.cdm.api.service.pager.Pager;
  19 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  20 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  21 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  22 import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
  23 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  24 import eu.etaxonomy.cdm.model.name.NonViralName;
  25 import eu.etaxonomy.cdm.model.name.Rank;
  26 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  27 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  28 import eu.etaxonomy.cdm.model.taxon.Synonym;
  29 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  30 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  31 import eu.etaxonomy.cdm.model.taxon.Taxon;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  35 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  36 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  37 import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
  38 import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
  39 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  40
  41
  42 public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
  43
  44         /**
  45          * Computes all taxon bases.
  46          * FIXME could substitute with list(Synonym.class, limit, start)
  47          * @param limit
  48          * @param start
  49          * @return
  50          */
  51         public List<Synonym> getAllSynonyms(int limit, int start);
  52
  53         /**
  54          * Computes all taxon bases.
  55          * FIXME could substitute with list(Taxon.class, limit,start)
  56          * @param limit
  57          * @param start
  58          * @return
  59          */
  60         public List<Taxon> getAllTaxa(int limit, int start);
  61
  62         /**
  63          * Computes all Taxon instances that do not have a taxonomic parent and has at least one child.
  64          * @param sec The concept reference that the taxon belongs to
  65          * @return The List<Taxon> of root taxa.
  66          * @deprecated obsolete when using taxonomicTree
  67          */
  68         public List<Taxon> getRootTaxa(ReferenceBase sec);
  69
  70
  71         /**
  72          * Computes all Taxon instances that do not have a taxonomic parent.
  73          * @param sec The concept reference that the taxon belongs to
  74          *
  75          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  76          * @return The List<Taxon> of root taxa.
  77          * @deprecated obsolete when using taxonomicTree
  78          */
  79         public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren);
  80
  81         /**
  82          * Computes all Taxon instances that do not have a taxonomic parent.
  83          * @param sec The concept reference that the taxon belongs to
  84          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  85          * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  86          * the misapplied name are not returned.<Br>Default: true.
  87          * @return The List<Taxon> of root taxa.
  88          * @deprecated obsolete when using taxonomicTree
  89          */
  90         public List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications);
  91
  92         /**
  93          * Computes all Taxon instances which name is of a certain Rank.
  94          * @param rank The rank of the taxon name
  95          * @param sec The concept reference that the taxon belongs to
  96          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  97          * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  98          * the misapplied name are not returned.<Br>Default: true.
  99          * @param propertyPaths
 100          *            properties to be initialized, For detailed description and
 101          *            examples <b>please refer to:</b>
 102          *            {@link BeanInitializer#initialize(Object, List)}. <Br>
 103          *            Default: true.
 104          * @return The List<Taxon> of root taxa.
 105          * @deprecated obsolete when using taxonomicTree
 106          */
 107         public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
 108
 109         /**
 110          * Computes all relationships.
 111          * @param limit
 112          * @param start
 113          * @return
 114          */
 115     public List<RelationshipBase> getAllRelationships(int limit, int start);
 116
 117         /**
 118          * Returns TaxonRelationshipType vocabulary
 119          * @return
 120          * @deprecated use TermService#getVocabulary(VocabularyType) instead
 121          */
 122         public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
 123
 124         /**
 125          * Returns a list of taxa that matches the name string and the sec reference
 126          * @param name the name string to search for
 127          * @param sec the taxons sec reference
 128          * @return a list of taxa matching the name and the sec reference
 129          */
 130         public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec);
 131
 132         /**
 133          * Changes an accepted taxon to a synonym of another taxon.
 134          *
 135          * @param oldTaxonNode
 136          *                              the <code>TaxonNode</code> of the accepted taxon that will be changed into a synonym
 137          * @param newAcceptedTaxonNode
 138          *                              the <code>TaxonNode</code> of the accepted taxon, the old taxon will become a synonym of
 139          * @param synonymType
 140          *                              <code>SynonymRelationshipType</code> to indicate whether hetero or homotypic
 141          * @param citation
 142          *                              the reference for this assumption
 143          * @param citationMicroReference
 144          *                              the micro citation
 145          * @return
 146          *                              the newly created synonym
 147          */
 148         public Synonym changeAcceptedTaxonToSynonym (TaxonNode oldTaxonNode, TaxonNode newAcceptedTaxonNode, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference);
 149
 150         /**
 151          * Swaps given synonym and accepted taxon.
 152          * In particular:
 153          * <ul>
 154          *              <li>A new accepted taxon with the synonyms name is created</li>
 155          *              <li>The synonym is deleted from the old accepted taxons synonym list</li>
 156          *              <li>A new synonym with the name of the old accepted taxon is created</li>
 157          *              <li>The newly created synonym get related to the newly created accepted taxon</li>
 158          * </ul>
 159          *
 160          * @param synonym
 161          * @param acceptedTaxon
 162          * @param synonymRelationshipType the relationship type the newly created synonym will have. Defaults to SYNONYM_OF
 163          */
 164         public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 165
 166         /**
 167          * Change a synonym into an accepted taxon and removes
 168          * the synonym relationship to the given accepted taxon.
 169          *
 170          * @param synonym
 171          *                              the synonym to change into an accepted taxon
 172          * @param acceptedTaxon
 173          *                              an accepted taxon, the synonym had a relationship to
 174          * @return
 175          *                              the newly created accepted taxon
 176          */
 177         public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 178
 179         /**
 180          * Change a synonym into a related concept
 181          *
 182          * @param synonym
 183          *                              the synonym to change into the concept taxon
 184          * @param toTaxon
 185          *                              the taxon the newly created concept should be related to
 186          * @param taxonRelationshipType
 187          *                              the type of relationship
 188          * @param citation
 189          * @param microcitation
 190          * @return
 191          *                              the newly created concept
 192          */
 193         public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, ReferenceBase citation, String microcitation);
 194
 195         /**
 196          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 197          * where the supplied taxon is relatedTo.
 198          *
 199          * @param taxon The taxon that is relatedTo
 200          * @param type The type of TaxonRelationship (can be null)
 201          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 202          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 203          * @param orderHints Properties to order by
 204          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 205          * @return a List of TaxonRelationship instances
 206          */
 207         public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 208
 209
 210
 211         /**
 212          * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
 213          * where the supplied taxon is relatedTo.
 214          *
 215          * @param taxon The taxon that is relatedTo
 216          * @param type The type of TaxonRelationship (can be null)
 217          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 218          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 219          * @param orderHints Properties to order by
 220          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 221          * @return a Pager of TaxonRelationship instances
 222          */
 223         public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 224
 225         /**
 226          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 227          * where the supplied taxon is relatedFrom.
 228          *
 229          * @param taxon The taxon that is relatedFrom
 230          * @param type The type of TaxonRelationship (can be null)
 231          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 232          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 233          * @param orderHints Properties to order by
 234          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 235          * @return a List of TaxonRelationship instances
 236          */
 237         public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 238
 239
 240         /**
 241          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 242          * where the supplied taxon is relatedFrom.
 243          *
 244          * @param taxon The taxon that is relatedFrom
 245          * @param type The type of TaxonRelationship (can be null)
 246          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 247          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 248          * @param orderHints Properties to order by
 249          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 250          * @return a Pager of TaxonRelationship instances
 251          */
 252         public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 253
 254         /**
 255          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 256          * where the supplied synonym is relatedFrom.
 257          *
 258          * @param taxon The synonym that is relatedFrom
 259          * @param type The type of SynonymRelationship (can be null)
 260          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 261          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 262          * * @param orderHints Properties to order by
 263          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 264          * @return a Pager of SynonymRelationship instances
 265          */
 266         public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 267
 268         /**
 269          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 270          * where the supplied taxon is relatedTo.
 271          *
 272          * @param taxon The taxon that is relatedTo
 273          * @param type The type of SynonymRelationship (can be null)
 274          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 275          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 276          * * @param orderHints Properties to order by
 277          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 278          * @return a Pager of SynonymRelationship instances
 279          */
 280         public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 281
 282         public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 283
 284         public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
 285
 286         /**
 287          * Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 288          *
 289          * @param clazz filter the results by class (or pass null to return all TaxonBase instances)
 290          * @param queryString
 291          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 292          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 293          * @param orderHints
 294          *            Supports path like <code>orderHints.propertyNames</code> which
 295          *            include *-to-one properties like createdBy.username or
 296          *            authorTeam.persistentTitleCache
 297          * @param propertyPaths properties to be initialized
 298          * @return a Pager Taxon instances
 299          * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 300          */
 301         public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 302
 303         /**
 304          * Returns a list of TaxonBase instances where the
 305          * taxon.name properties match the parameters passed.
 306          *
 307          * @param clazz optionally filter by class
 308          * @param uninomial
 309          * @param infragenericEpithet
 310          * @param specificEpithet
 311          * @param infraspecificEpithet
 312          * @param rank
 313          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 314          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 315          * @return a Pager of TaxonBase instances
 316          */
 317         public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 318
 319         /**
 320          * Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)
 321          * that match the properties specified in the configurator.
 322          * @param configurator
 323          * @return
 324          */
 325         public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator);
 326
 327         /**
 328          *
 329          * @param taxon
 330          * @param size
 331          * @param height
 332          * @param widthOrDuration
 333          * @param mimeTypes
 334          * @return
 335          */
 336         public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
 337
 338         public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
 339         /**
 340          * returns a list of inferred synonyms concerning the taxon with synonymrelationshiptype type
 341          * @param tree
 342          * @param taxon
 343          * @param type
 344          * @return
 345          */
 346         public List<Synonym> createInferredSynonyms(TaxonomicTree tree, Taxon taxon, SynonymRelationshipType type);
 347         /**
 348          * returns a list of all inferred synonyms (inferred epithet, inferred genus and potential combination) concerning the taxon
 349          * @param tree
 350          * @param taxon
 351          * @return
 352          */
 353         public List<Synonym> createAllInferredSynonyms(TaxonomicTree tree, Taxon taxon);
 354
 355         public int countAllRelationships();
 356
 357         public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
 358         public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath);
 359         public String getPhylumName(TaxonNameBase name);
 360
 361         public long deleteSynonymRelationships(Synonym syn);
 362         /**
 363          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 364          * depending on direction, where the supplied taxon is relatedTo or the supplied synonym is relatedFrom.
 365          *
 366          * @param taxonBase The taxon or synonym that is relatedTo or relatedFrom
 367          * @param type The type of SynonymRelationship (can be null)
 368          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 369          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 370          * @param orderHints Properties to order by
 371          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 372          * @param direction The direction of the relationship
 373          * @return a List of SynonymRelationship instances
 374          */
 375         public List<SynonymRelationship> listSynonymRelationships(
 376                         TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
 377                         List<OrderHint> orderHints, List<String> propertyPaths, Direction direction);
 378 }