cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/ITaxonService.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.io.IOException;
  13 import java.util.EnumSet;
  14 import java.util.List;
  15 import java.util.Set;
  16 import java.util.UUID;
  17
  18 import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
  19 import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration;
  20 import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
  21 import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
  22 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  23 import eu.etaxonomy.cdm.api.service.dto.IdentifiedEntityDTO;
  24 import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO;
  25 import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
  26 import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;
  27 import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
  28 import eu.etaxonomy.cdm.api.service.pager.Pager;
  29 import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;
  30 import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
  31 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  32 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  33 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  34 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.MarkerType;
  37 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  38 import eu.etaxonomy.cdm.model.description.Feature;
  39 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  40 import eu.etaxonomy.cdm.model.location.NamedArea;
  41 import eu.etaxonomy.cdm.model.media.Media;
  42 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  43 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  44 import eu.etaxonomy.cdm.model.name.Rank;
  45 import eu.etaxonomy.cdm.model.name.TaxonName;
  46 import eu.etaxonomy.cdm.model.reference.Reference;
  47 import eu.etaxonomy.cdm.model.taxon.Classification;
  48 import eu.etaxonomy.cdm.model.taxon.Synonym;
  49 import eu.etaxonomy.cdm.model.taxon.SynonymType;
  50 import eu.etaxonomy.cdm.model.taxon.Taxon;
  51 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  53 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  54 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  55 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  56 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  57 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  58 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  59 import eu.etaxonomy.cdm.persistence.query.TaxonTitleType;
  60
  61
  62 public interface ITaxonService
  63              extends IIdentifiableEntityService<TaxonBase>, IPublishableService<TaxonBase>{
  64
  65     /**
  66      * {@inheritDoc}
  67      * <BR><BR>
  68      * NOTE: Also taxa with <code>publish=false</code> are returned.
  69      */
  70     @Override
  71     public TaxonBase load(UUID uuid, List<String> propertyPaths);
  72
  73     /**
  74      * Returns a list of taxa that matches the name string and the sec reference
  75      * @param name the name string to search for
  76      * @param sec the taxons sec reference
  77      * @return a list of taxa matching the name and the sec reference
  78      */
  79     public List<TaxonBase> searchByName(String name, boolean includeUnpublished, Reference sec);
  80
  81     /**
  82      * Swaps given synonym and accepted taxon.
  83      * In particular:
  84      * <ul>
  85      *          <li>A new accepted taxon with the synonyms name is created</li>
  86      *          <li>The synonym is deleted from the old accepted taxons synonym list</li>
  87      *          <li>A new synonym with the name of the old accepted taxon is created</li>
  88      *          <li>The newly created synonym get related to the newly created accepted taxon</li>
  89      * </ul>
  90      *
  91      * @param synonym
  92      * @param acceptedTaxon
  93      * @return
  94      */
  95     public UpdateResult swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
  96
  97     /**
  98      * Changes a synonym into an accepted taxon and removes
  99      * the synonym relationship to the given accepted taxon.
 100      * Other synonyms homotypic to the synonym to change are
 101      * moved to the same new accepted taxon as homotypic
 102      * synonyms. The new accepted taxon has the same name and
 103      * the same sec reference as the old synonym.<BR>
 104      * If the given accepted taxon and the synonym are homotypic
 105      * to each other an exception may be thrown as taxonomically it doesn't
 106      * make sense to have two accepted taxa in the same homotypic group
 107      * but also it is than difficult to decide how to handle other names
 108      * in the homotypic group. It is up to the implementing class to
 109      * handle this situation via an exception or in another way.
 110      *
 111      *
 112      * @param synonym
 113      *                          the synonym to change into an accepted taxon
 114      * @param acceptedTaxon
 115      *                          an accepted taxon, the synonym had a relationship to
 116      * @param deleteSynonym
 117      *                  if true the method tries to delete the old synonym from the database
 118      * @return
 119      *                  the newly created accepted taxon
 120      * @throws IllegalArgumentException
 121      *                  if the given accepted taxon and the synonym are homotypic
 122      *              to each other an exception may be thrown as taxonomically it doesn't
 123      *                  make sense to have two accepted taxa in the same homotypic group
 124      *          but also it is than difficult to decide how to handle other names
 125      *          in the homotypic group. It is up to the implementing class to
 126      *          handle this situation via an exception or in another way.
 127      */
 128     public UpdateResult changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym) throws HomotypicalGroupChangeException;
 129
 130     /**
 131      * @param synonymUuid
 132      * @param acceptedTaxonUuid
 133      * @param newParentNodeUuid
 134      * @param deleteSynonym
 135      * @return
 136      * @throws HomotypicalGroupChangeException
 137      */
 138     public UpdateResult changeSynonymToAcceptedTaxon(UUID synonymUuid, UUID acceptedTaxonUuid, UUID newParentNodeUuid,
 139             boolean deleteSynonym)
 140             throws HomotypicalGroupChangeException;
 141
 142     /**
 143      * Change a synonym into a related concept
 144      *
 145      * @param synonym
 146      *                          the synonym to change into the concept taxon
 147      * @param toTaxon
 148      *                          the taxon the newly created concept should be related to
 149      * @param taxonRelationshipType
 150      *                          the type of relationship
 151      * @param reference
 152      * @param microReference
 153      * @return
 154      *                          update result with the newly created concept
 155      */
 156     public UpdateResult changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference reference, String microReference);
 157
 158     /**
 159      *
 160      * Change a related concept into synonym
 161      *
 162      * @param synonym
 163      *                          the concept taxon to change into a synonym
 164      * @param toTaxon
 165      *                          the taxon the newly created synonym should be related to
 166      * @param oldRelationshipType
 167      *              the type of old concept relationship
 168      * @param synonymRelationshipType
 169      *                          the type of new synonym relationship
 170      *
 171      * @return
 172      *                          update result with the newly created synonym
 173      * @throws DataChangeNoRollbackException
 174      */
 175   public        UpdateResult changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon,
 176              TaxonRelationshipType oldRelationshipType,
 177             SynonymType synonymType) throws DataChangeNoRollbackException;
 178
 179     /**
 180      * Changes the homotypic group of a synonym into the new homotypic group.
 181      * All relations to taxa are updated correctly depending on the homotypic
 182      * group of the accepted taxon. <BR>
 183      * All existing basionym relationships to and from this name are removed.<BR>
 184      * If the parameter <code>targetTaxon</code> is defined, the synonym is
 185      * added to this taxon irrespctive of if it has been related to this
 186      * taxon before.<BR>
 187      * If <code>setBasionymRelationIfApplicable</code> is true a basionym relationship
 188      * between the existing basionym(s) of the new homotypic group and the synonyms name
 189      * is added.<BR>
 190      *
 191      * @param synonym
 192      * @param newHomotypicalGroup
 193      * @param taxon
 194      * @param setBasionymRelationIfApplicable
 195      */
 196     public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup,
 197             Taxon targetTaxon, boolean setBasionymRelationIfApplicable);
 198
 199     /**
 200      * See {@link #moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)}
 201      * @param oldSynonym
 202      * @param newTaxon
 203      * @param moveHomotypicGroup
 204      * @param newSynonymType
 205      * @return
 206      * @throws HomotypicalGroupChangeException
 207      */
 208     public UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym, Taxon newTaxon, boolean moveHomotypicGroup,
 209             SynonymType newSynonymType) throws HomotypicalGroupChangeException;
 210
 211
 212     /**
 213      * Moves a synonym to another taxon and removes the old synonym relationship.
 214      *
 215      * @param oldSynonym the old synonym to move.
 216      * @param newTaxon the taxon the synonym will be moved to
 217      * @param moveHomotypicGroup if the synonym belongs to a homotypic group with other synonyms and
 218      *          <code>moveHomotypicGroup</code> is <code>true</code> all these synonyms are moved to the new taxon,
 219      *          if <code>false</code> a {@link HomotypicalGroupChangeException} is thrown.
 220      *          <code>moveHomotypicGroup</code> has no effect if the synonym is the only synonym in it's homotypic group.
 221      * @param newSynonymType the synonym type of the new synonyms. Default is
 222      *          {@link SynonymType#HETEROTYPIC_SYNONYM_OF() heterotypic}.
 223      * @param newSecundum The secundum for the new synonyms).
 224      * @param newSecundumDetail The secundum micro reference for the new synonym(s).
 225      * @param keepSecundumIfUndefined if no <code>newSecundum</code> and/or no <code>newSecundumDetail</code>
 226      *          is defined they are taken from the old synonym(s) if <code>keepSecundumIfUndefined</code> is
 227      *          <code>true</code>. If <code>false</code> the secundum and the secundum detail will be taken
 228      *          only from the <code>newSecundum</code> and <code>newSecundumDetail</code> even if they are
 229      *      undefined (<code>null</code>).
 230      * @return The new synonym relationship. If <code>moveHomotypicGroup</code> is <code>true</code> additionally
 231      *          created new synonym relationships must be retrieved separately from the new taxon.
 232      * @throws HomotypicalGroupChangeException Exception is thrown if (1) synonym is homotypic to the old accepted taxon or
 233      *          (2) synonym is in homotypic group with other synonyms and <code>moveHomotypicGroup</code> is false
 234      */
 235     public UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym, Taxon newTaxon, boolean moveHomotypicGroup,
 236             SynonymType newSynonymType, Reference newSecundum,
 237             String newSecundumDetail, boolean keepSecundumIfUndefined) throws HomotypicalGroupChangeException;
 238
 239
 240     /**
 241      * @param oldSynonym
 242      * @param newTaxonUUID
 243      * @param moveHomotypicGroup
 244      * @param newSynonymType
 245      * @param reference
 246      * @param referenceDetail
 247      * @param keepReference
 248      * @return
 249      * @throws HomotypicalGroupChangeException
 250      *
 251      * @see {@link #moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)}
 252      */
 253     public UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym,
 254             UUID newTaxonUUID, boolean moveHomotypicGroup,
 255             SynonymType newSynonymType,
 256             Reference newSecundum, String newSecundumDetail, boolean keepSecundumIfUndefined)
 257             throws HomotypicalGroupChangeException;
 258
 259     /**
 260      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 261      * where the supplied taxon is relatedTo.
 262      *
 263      * @param taxon The taxon that is relatedTo
 264      * @param type The type of TaxonRelationship (can be null)
 265      * @param includeUnpublished should unpublished related taxa also be returned?
 266      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 267      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 268      * @param orderHints Properties to order by
 269      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 270      * @return a List of TaxonRelationship instances
 271      */
 272     public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 273             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 274
 275
 276     /**
 277      * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
 278      * where the supplied taxon is relatedTo.
 279      *
 280      * @param taxon The taxon that is relatedTo
 281      * @param type The type of TaxonRelationship (can be null)
 282      * @param includeUnpublished should unpublished related taxa also be returned?
 283      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 284      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 285      * @param orderHints Properties to order by
 286      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 287      * @return a Pager of TaxonRelationship instances
 288      */
 289     public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 290             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 291
 292     /**
 293      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 294      * where the supplied taxon is relatedFrom.
 295      *
 296      * @param taxon The taxon that is relatedFrom
 297      * @param type The type of TaxonRelationship (can be null)
 298      * @param includeUnpublished should unpublished related taxa also be returned?
 299      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 300      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 301      * @param orderHints Properties to order by
 302      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 303      * @return a List of TaxonRelationship instances
 304      */
 305     public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 306             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 307
 308
 309     /**
 310      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 311      * where the supplied taxon is relatedFrom.
 312      *
 313      * @param taxon The taxon that is relatedFrom
 314      * @param type The type of TaxonRelationship (can be null)
 315      * @param includeUnpublished should unpublished related taxa also be returned?
 316      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 317      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 318      * @param orderHints Properties to order by
 319      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 320      * @return a Pager of TaxonRelationship instances
 321      */
 322     public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 323             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 324
 325     /**
 326      * lists all taxa which are related to the <code>taxon</code> given as
 327      * parameter.
 328      *
 329      * @param taxon
 330      * @param includeRelationships
 331      * @param maxDepth
 332      *            <code>1</code> for one level, <code>null</code> for infinite
 333      *            depth, <code>0</code> will completely omit collecting related taxa.
 334      * @param limit
 335      * @param start
 336      * @param propertyPaths
 337      * @return
 338      */
 339     public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,
 340             boolean includeUnpublished, Integer limit, Integer start, List<String> propertyPaths);
 341
 342
 343     /**
 344      * Returns all or a page of all taxon concept relationships in the database.
 345      * The result can be filtered by relationship types.
 346      *
 347      * @param types The taxon relationship type filter, if <code>null</code> no filter is set, if empty the result will also be empty
 348      * @param pageSize the page size
 349      * @param pageStart the number of the start page
 350      * @param orderHints the order hints
 351      * @param propertyPaths the property path to initialize the resulting objects
 352      * @return list of taxon relationships matching the filter criteria
 353      */
 354     public List<TaxonRelationship> listTaxonRelationships(Set<TaxonRelationshipType> types,
 355             Integer pageSize, Integer pageStart, List<OrderHint> orderHints, List<String> propertyPaths);
 356
 357     /**
 358      * Lists all classifications the given taxon/synonym is used in{@link Synonym}
 359      *
 360      * @param taxonBase
 361      * @param limit
 362      * @param start
 363      * @param propertyPaths
 364      * @return
 365      */
 366     public List<Classification> listClassifications(TaxonBase taxonBase, Integer limit, Integer start, List<String> propertyPaths);
 367
 368     /**
 369      * Returns the Synonyms (with the given synonym relationship type, if this argument is supplied)
 370      * that do have the supplied taxon as accepted taxon.
 371      *
 372      * @param taxon The accepted taxon
 373      * @param type The type of Synonym (can be null)
 374      * @param pageSize The maximum number of synonyms returned (can be null for returning synonyms)
 375      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 376      * * @param orderHints Properties to order by
 377      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 378      * @return a Pager of {@link Synonym} instances
 379      */
 380     public Pager<Synonym> getSynonyms(Taxon taxon, SynonymType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 381
 382     /**
 383      * This method returns in the first entry the list of synonyms of the
 384      * homotypic group of the accepted taxon. All other entries represent the lists of heterotypic
 385      * synonym groups. For detailed information about these 2 groups see
 386      * {@link #getHomotypicSynonymsByHomotypicGroup(Taxon, List)} and
 387      * {@link #getHeterotypicSynonymyGroups(Taxon, List)}
 388      *
 389      * @see                     #getSynonyms()
 390      * @see                     SynonymType#HETEROTYPIC_SYNONYM_OF()
 391      * @see                     eu.etaxonomy.cdm.model.name.HomotypicalGroup
 392
 393      * @param taxon the accepted taxon
 394      * @param propertyPaths the property path
 395      * @return the list of groups of synonyms
 396      */
 397     public List<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 398
 399
 400     /**
 401      * Returns the list of all synonyms that share the same homotypical group with the given taxon.
 402      * Only those homotypic synonyms are returned that do have a synonym relationship with the accepted taxon.
 403      * @param taxon
 404      * @param propertyPaths
 405      * @return
 406      */
 407     public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 408
 409     /**
 410      * Returns the ordered list of all {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical groups}
 411      * that contain {@link Synonym synonyms} that are heterotypic to the given taxon.
 412      * {@link eu.etaxonomy.cdm.model.name.TaxonName Taxon names} of heterotypic synonyms
 413      * belong to a homotypical group which cannot be the homotypical group to which the
 414      * taxon name of the given taxon belongs. This method does not return the homotypic group the given
 415      * taxon belongs to.<BR>
 416      * This method does neglect the type of synonym relationship that is defined between the given taxon
 417      * and the synonym. So the synonym relationship may be homotypic however a synonym is returned
 418      * in one of the result lists as long as the synonym does not belong to the same homotypic group as
 419      * the given taxon.<BR>
 420      * The list returned is ordered according to the date of publication of the
 421      * first published name within each homotypical group.
 422      *
 423      * @see                     #getHeterotypicSynonymyGroups()
 424      * @see                     #getSynonyms()
 425      * @see                     SynonymType#HETEROTYPIC_SYNONYM_OF()
 426      * @see                     eu.etaxonomy.cdm.model.name.HomotypicalGroup
 427
 428      * @param taxon
 429      * @param propertyPaths
 430      * @return
 431      */
 432     public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
 433
 434     /**
 435      * Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 436      *
 437      * @param clazz filter the results by class (or pass null to return all TaxonBase instances)
 438      * @param queryString
 439      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 440      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 441      * @param orderHints
 442      *            Supports path like <code>orderHints.propertyNames</code> which
 443      *            include *-to-one properties like createdBy.username or
 444      *            authorTeam.persistentTitleCache
 445      * @param propertyPaths properties to be initialized
 446      * @return a Pager Taxon instances
 447      * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 448      */
 449     @Override
 450     public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 451
 452     /**
 453      * Returns a list of TaxonBase instances where the
 454      * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 455      * <i>null</i> will search for those taxa with a value of null in that field
 456      *
 457      * @param clazz optionally filter by class (can be null to return all taxa)
 458      * @param uninomial
 459      * @param infragenericEpithet
 460      * @param specificEpithet
 461      * @param infraspecificEpithet
 462      * @param rank
 463      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 464      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 465      * @return a list of TaxonBase instances
 466      */
 467     public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
 468
 469     /**
 470      * Returns a list of TaxonBase instances where the
 471      * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 472      * <i>null</i> will search for those taxa with a value of null in that field
 473      *
 474      * @param clazz optionally filter by class
 475      * @param uninomial
 476      * @param infragenericEpithet
 477      * @param specificEpithet
 478      * @param infraspecificEpithet
 479      * @param rank
 480      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 481      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 482      * @return a List of TaxonBase instances
 483      */
 484     public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
 485
 486     /**
 487      * Returns a list of IdentifiableEntity instances (in particular, TaxonName and TaxonBase instances)
 488      * that match the properties specified in the configurator.
 489      * @param configurator
 490      * @return
 491      */
 492     public Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator);
 493
 494     /**
 495      * performes a union searches for TaxonBase instances on all available
 496      * free text indexes. At the time of writing this documentation it combines
 497      * {@link #findByDescriptionElementFullText(Class, String, Classification, List, List, boolean, Integer, Integer, List, List)}
 498      * and {@link #findByFullText(Class, String, Classification, List, boolean, Integer, Integer, List, List)
 499      *
 500      * @param queryString
 501      *            the query string
 502      * @param classification
 503      *            Additional filter criterion: If a taxonomic classification
 504      *            three is specified here the result set will only contain taxa
 505      *            of the given classification
 506      * @param languages
 507      *            Additional filter criterion: Search only in these languages.
 508      *            Not all text fields in the cdm model are multilingual, thus
 509      *            this setting will only apply to the multilingiual fields.
 510      *            Other fields are searched nevertheless if this parameter is
 511      *            set or not.
 512      * @param highlightFragments
 513      *            TODO
 514      * @param pageSize
 515      *            The maximum number of objects returned (can be null for all
 516      *            objects)
 517      * @param pageNumber
 518      *            The offset (in pageSize chunks) from the start of the result
 519      *            set (0 - based)
 520      * @param orderHints
 521      *            Supports path like <code>orderHints.propertyNames</code> which
 522      *            include *-to-one properties like createdBy.username or
 523      *            authorTeam.persistentTitleCache
 524      * @param propertyPaths
 525      *            properties to initialize - see
 526      *            {@link IBeanInitializer#initialize(Object, List)}
 527      * @return a paged list of instances of type T matching the queryString and
 528      *         the additional filter criteria
 529      * @return
 530      * @throws LuceneCorruptIndexException
 531      * @throws IOException
 532      * @throws LuceneParseException
 533      * @throws LuceneMultiSearchException
 534      * @deprecated this search should fully be covered by the new method
 535      *      {@link #findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List)}
 536      *      , maybe we should rename this latter method to give it a more meaningful name
 537      */
 538     @Deprecated
 539     public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,
 540             Classification classification, boolean includeUnpublished, List<Language> languages, boolean highlightFragments,
 541             Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException, LuceneMultiSearchException;
 542
 543     /**
 544      * Searches for TaxonBase instances using the TaxonBase free text index.
 545      *
 546      * <h4>This is an experimental feature, it may be moved, modified, or even
 547      * removed in future releases!!!</h4>
 548      *
 549      * @param clazz
 550      *            Additional filter criterion: The specific TaxonBase subclass
 551      *            to search for
 552      * @param queryString
 553      *            the query string
 554      * @param classification
 555      *            Additional filter criterion: If a taxonomic classification
 556      *            three is specified here the result set will only contain taxa
 557      *            of the given classification
 558      * @param languages
 559      *            Additional filter criterion: Search only in these languages.
 560      *            Not all text fields in the cdm model are multilingual, thus
 561      *            this setting will only apply to the multilingiual fields.
 562      *            Other fields are searched nevertheless if this parameter is
 563      *            set or not.
 564      * @param highlightFragments
 565      *            TODO
 566      * @param pageSize
 567      *            The maximum number of objects returned (can be null for all
 568      *            objects)
 569      * @param pageNumber
 570      *            The offset (in pageSize chunks) from the start of the result
 571      *            set (0 - based)
 572      * @param orderHints
 573      *            Supports path like <code>orderHints.propertyNames</code> which
 574      *            include *-to-one properties like createdBy.username or
 575      *            authorTeam.persistentTitleCache
 576      * @param propertyPaths
 577      *            properties to initialize - see
 578      *            {@link IBeanInitializer#initialize(Object, List)}
 579      * @return a paged list of instances of type T matching the queryString and
 580      *         the additional filter criteria
 581      * @throws LuceneCorruptIndexException
 582      * @throws IOException
 583      * @throws LuceneParseException
 584      */
 585     public Pager<SearchResult<TaxonBase>> findByFullText(Class<? extends TaxonBase> clazz, String queryString,
 586             Classification classification, boolean includeUnpublished, List<Language> languages,
 587             boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 588             List<String> propertyPaths) throws IOException, LuceneParseException;
 589
 590
 591     /**
 592      * @param areaFilter
 593      * @param statusFilter
 594      * @param classification
 595      *            Additional filter criterion: If a taxonomic classification
 596      *            three is specified here the result set will only contain taxa
 597      *            of the given classification
 598      * @param highlightFragments
 599      * @param pageSize
 600      *            The maximum number of objects returned (can be null for all
 601      *            objects)
 602      * @param pageNumber
 603      *            The offset (in pageSize chunks) from the start of the result
 604      *            set (0 - based)
 605      * @param orderHints
 606      *            Supports path like <code>orderHints.propertyNames</code> which
 607      *            include *-to-one properties like createdBy.username or
 608      *            authorTeam.persistentTitleCache
 609      * @param propertyPath
 610      *            Common properties to initialize the instances of the
 611      *            CDM types ({@link Taxon} and {@link Synonym}
 612      *            this method can return - see {@link IBeanInitializer#initialize(Object, List)}
 613      * @return a paged list of instances of {@link Taxon} instances
 614      * @throws IOException
 615      * @throws LuceneParseException
 616      */
 617     public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTerm> statusFilter,
 618             Classification classification,
 619             Integer pageSize, Integer pageNumber,
 620             List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException;
 621
 622     /**
 623      * Searches for TaxonBase instances using the TaxonBase free text index.
 624      *
 625      *
 626      *
 627      * <h4>This is an experimental feature, it may be moved, modified, or even
 628      * removed in future releases!!!</h4>
 629      * @param searchModes
 630      *            Additional filter criterion: defaults to [doTaxa] if set null
 631      * @param queryString
 632      *            the query string
 633      * @param classification
 634      *            Additional filter criterion: If a taxonomic classification
 635      *            three is specified here the result set will only contain taxa
 636      *            of the given classification
 637      * @param namedAreas
 638      * @param languages
 639      *            Additional filter criterion: Search only in these languages.
 640      *            Not all text fields in the cdm model are multilingual, thus
 641      *            this setting will only apply to the multilingiual fields.
 642      *            Other fields are searched nevertheless if this parameter is
 643      *            set or not.
 644      * @param highlightFragments
 645      *            TODO
 646      * @param pageSize
 647      *            The maximum number of objects returned (can be null for all
 648      *            objects)
 649      * @param pageNumber
 650      *            The offset (in pageSize chunks) from the start of the result
 651      *            set (0 - based)
 652      * @param orderHints
 653      *            Supports path like <code>orderHints.propertyNames</code> which
 654      *            include *-to-one properties like createdBy.username or
 655      *            authorTeam.persistentTitleCache
 656      * @param propertyPath
 657      *            Common properties to initialize the instances of the
 658      *            CDM types ({@link Taxon} and {@link Synonym}
 659      *            this method can return - see {@link IBeanInitializer#initialize(Object, List)}
 660      * @return a paged list of instances of {@link Taxon}, {@link Synonym}, matching the queryString and
 661      *         the additional filter criteria
 662      * @throws LuceneCorruptIndexException
 663      * @throws IOException
 664      * @throws LuceneParseException
 665      * @throws LuceneMultiSearchException
 666      */
 667     public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(
 668             EnumSet<TaxaAndNamesSearchMode> searchModes,
 669             String queryString, Classification classification, Set<NamedArea> namedAreas, Set<PresenceAbsenceTerm> distributionStatus,
 670             List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 671             List<String> propertyPaths) throws IOException, LuceneParseException, LuceneMultiSearchException;
 672
 673     /**
 674      * Searches for TaxonBase instances by using the DescriptionElement free text index.
 675      *
 676      * <h4>This is an experimental feature, it may be moved, modified, or even
 677      * removed in future releases!!!</h4>
 678      *
 679      * @param clazz
 680      *            Additional filter criterion:
 681      * @param queryString
 682      *            the query string to filter by
 683      * @param classification
 684      *            Additional filter criterion: If a taxonomic classification
 685      *            three is specified here the result set will only contain taxa
 686      *            of the given classification
 687      * @param features
 688      *            TODO
 689      * @param languages
 690      *            Additional filter criterion: Search only in these languages.
 691      *            Not all text fields in the cdm model are multilingual, thus
 692      *            this setting will only apply to the multilingiual fields.
 693      *            Other fields are searched nevertheless if this parameter is
 694      *            set or not.
 695      * @param highlightFragments
 696      *            TODO
 697      * @param pageSize
 698      *            The maximum number of objects returned (can be null for all
 699      *            objects)
 700      * @param pageNumber
 701      *            The offset (in pageSize chunks) from the start of the result
 702      *            set (0 - based)
 703      * @param orderHints
 704      *            Supports path like <code>orderHints.propertyNames</code> which
 705      *            include *-to-one properties like createdBy.username or
 706      *            authorTeam.persistentTitleCache
 707      * @param propertyPaths
 708      *            properties to initialize - see
 709      *            {@link IBeanInitializer#initialize(Object, List)}
 710      * @return a paged list of instances of type T matching the queryString and
 711      *         the additional filter criteria
 712      * @throws IOException
 713      * @throws LuceneCorruptIndexException
 714      * @throws LuceneParseException
 715      */
 716     public Pager<SearchResult<TaxonBase>> findByDescriptionElementFullText(Class<? extends DescriptionElementBase> clazz, String queryString, Classification classification, List<Feature> features, List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException;
 717
 718
 719     /**
 720      *
 721      * @param taxon
 722      * @param size
 723      * @param height
 724      * @param widthOrDuration
 725      * @param mimeTypes
 726      * @return
 727      *
 728      * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
 729      */
 730     @Deprecated
 731     public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
 732
 733
 734     /**
 735      * Lists all Media found in an any TaxonDescription associated with this
 736      * taxon.
 737      *
 738      * @param taxon
 739      * @param includeRelationships
 740      *            the given list of TaxonRelationshipEdges will be taken into
 741      *            account when retrieving media associated with the given taxon.
 742      *            Can be NULL.
 743      * @param limitToGalleries
 744      *            whether to take only TaxonDescription into account which are
 745      *            marked as gallery
 746      * @return
 747      * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
 748      */
 749     @Deprecated
 750     public List<Media> listTaxonDescriptionMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, List<String> propertyPath);
 751
 752     /**
 753      * Lists all Media found in an any TaxonDescription, NameDescription,
 754      * SpecimenOrObservationBase, DnaSample Chromatograms, etc. associated with this taxon.
 755      *
 756      * @param taxon
 757      * @param includeRelationships
 758      *            the given list of TaxonRelationshipEdges will be taken into
 759      *            account when retrieving media associated with the given taxon.
 760      *            Can be NULL.
 761      * @param limitToGalleries
 762      *            whether to take only descriptions into account which are
 763      *            marked as gallery, can be NULL
 764      * @param includeTaxonDescriptions
 765      *            whether to take TaxonDescriptions into account, can be NULL
 766      * @param includeOccurrences
 767      *          whether to take TaxonDescriptions into account, can be NULL
 768      * @param includeTaxonNameDescriptions
 769      *       whether to take TaxonNameDescriptions into account, can be NULL
 770      * @param propertyPath
 771      * @return
 772      */
 773     public List<Media> listMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
 774             Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,
 775             Boolean includeTaxonNameDescriptions, List<String> propertyPath);
 776
 777     public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
 778
 779     /**
 780      * Returns the TaxonBase with the given UUID
 781      * using the given match mode and initialization strategy
 782      *
 783      * @param uuid
 784      * @param propertyPaths
 785      * @return
 786      */
 787     public TaxonBase findTaxonByUuid(UUID uuid, List<String> propertyPaths);
 788
 789     /**
 790      * Counts the number of synonyms
 791      * @param onlyAttachedToTaxon if <code>true</code> only those synonyms being attached to
 792      * an accepted taxon are counted
 793      * @return the number of synonyms
 794      */
 795     public int countSynonyms(boolean onlyAttachedToTaxon);
 796
 797     public List<TaxonName> findIdenticalTaxonNames(List<String> propertyPath);
 798
 799     public List<TaxonName> findIdenticalTaxonNameIds(List<String> propertyPath);
 800 //
 801 //    public String getPhylumName(TaxonName name);
 802
 803     /**
 804      * Returns all {@link Taxon taxa} which are {@link TaxonRelationshipType#CONGRUENT_TO() congruent} or
 805      * {@link TaxonRelationshipType#INCLUDES() included} in the taxon represented by the given taxon uuid.
 806      * The result also returns the path to these taxa represented by the uuids of
 807      * the {@link TaxonRelationshipType taxon relationships types} and doubtful information.
 808      * If classificationUuids is set only taxa of classifications are returned which are included
 809      * in the given {@link Classification classifications}. ALso the path to these taxa may not include
 810      * taxa from other classifications.
 811      * @param taxonUuid uuid of the original taxon
 812      * @param classificationUuids List of uuids of classifications used as a filter
 813      * @param includeDoubtful set to <code>true</code> if also doubtfully included taxa should be included in the result
 814      * @return a DTO which includes a list of taxa with the pathes from the original taxon to the given taxon as well
 815      * as doubtful and date information. The original taxon is included in the result.
 816      */
 817     public IncludedTaxaDTO listIncludedTaxa(UUID taxonUuid, IncludedTaxonConfiguration configuration);
 818
 819
 820    /**
 821      * Removes a synonym.<BR><BR>
 822      *
 823      * In detail it removes
 824      *  <li>the synonym concept</li>
 825      *  <BR><BR>
 826      *  If <code>removeNameIfPossible</code> is true
 827      *  it also removes the synonym name if it is not used in any other context
 828      *  (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)<BR><BR>
 829      *  If <code>newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name
 830      *  is not deleted and the name is homotypic to the taxon
 831      *  the name is moved to a new homotypic group.<BR><BR>
 832      *
 833      *  If synonym is <code>null</code> the method has no effect.
 834      *
 835      * @param taxon
 836      * @param synonym
 837      * @param removeNameIfPossible
 838      * @return deleteResult
 839      *
 840      */
 841     public DeleteResult deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config);
 842
 843     /**
 844      * Removes a synonym.
 845      *
 846      * The method essentially loads the synonym and calls the
 847      * {@link #deleteSynonym(Synonym, SynonymDeletionConfigurator) deleteSynonym} method
 848      *
 849      * @param synonymUuid
 850      * @param config
 851      * @return
 852      */
 853     public DeleteResult deleteSynonym(UUID synonymUuid, SynonymDeletionConfigurator config);
 854
 855     /**
 856      * @param tnb
 857      * @return
 858      */
 859     public Taxon findBestMatchingTaxon(String taxonName);
 860
 861     public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config);
 862
 863     public Synonym findBestMatchingSynonym(String taxonName, boolean includeUnpublished);
 864
 865      public List<UuidAndTitleCache<IdentifiableEntity>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator);
 866
 867     /**
 868      * Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
 869      * @param taxon
 870      * @param tree
 871      * @return list of inferred synonyms
 872      */
 873     public List<Synonym> createInferredSynonyms(Taxon taxon, Classification tree, SynonymType type, boolean doWithMisappliedNames);
 874
 875     /**
 876      * Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database
 877      * @param taxon
 878      * @param tree
 879      * @param iDatabase
 880      * @return list of inferred synonyms
 881      */
 882     public List<Synonym>  createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames);
 883
 884     public Taxon findAcceptedTaxonFor(UUID synonymUuid, UUID classificationUuid, List<String> propertyPaths);
 885
 886     public List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config);
 887
 888
 889     /**
 890      * @param clazz the optional {@link TaxonBase} subclass
 891      * @param identifier the identifier string
 892      * @param identifierType the identifier type
 893      * @param subtreeFilter filter on a classification subtree (TaxonNode)
 894      * @param matchmode the match mode for the identifier string
 895      * @param includeEntity should the taxon as an object be included in the result
 896      * @param pageSize page size
 897      * @param pageNumber page number
 898      * @param propertyPaths property path for initializing the returned taxon object (requires includeEntity=true)
 899      * @return the resulting {@link IdentifiedEntityDTO} pager
 900      * @see IIdentifiableEntityService#findByIdentifier(Class, String, DefinedTerm, MatchMode, boolean, Integer, Integer, List)
 901      */
 902     public <S extends TaxonBase> Pager<IdentifiedEntityDTO<S>> findByIdentifier(
 903                         Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,
 904                         MatchMode matchmode, boolean includeEntity, Integer pageSize,
 905                         Integer pageNumber,     List<String> propertyPaths);
 906
 907     /**
 908      * Returns a pager for {@link MarkedEntityDTO DTOs} that hold the marker including type, title and uuid
 909      * and the according {@link TaxonBase} information (uuid, title and the taxon object itself (optional)).
 910      *
 911      * @param clazz The optional {@link TaxonBase} subclass
 912      * @param markerType the obligatory marker type, if not given, the results will always be empty
 913      * @param markerValue the optional
 914      * @param subtreeFilter filter on a classification subtree (TaxonNode)
 915      * @param includeEntity should the taxon as an object be included in the result
 916      * @param titleType which label to give the returned entity, taxon.titleCache, name.titleCache or name.nameCache
 917      * @param pageSize page size
 918      * @param pageNumber page number
 919      * @param propertyPaths property path for initializing the returned taxon object (requires includeEntity=true)
 920      * @return the resulting {@link MarkedEntityDTO} pager
 921      * @see IIdentifiableEntityService#findByMarker(Class, MarkerType, Boolean, boolean, Integer, Integer, List)
 922      */
 923     public <S extends TaxonBase> Pager<MarkedEntityDTO<S>> findByMarker(
 924             Class<S> clazz, MarkerType markerType, Boolean markerValue,
 925             TaxonNode subtreeFilter, boolean includeEntity, TaxonTitleType titleType,
 926             Integer pageSize, Integer pageNumber, List<String> propertyPaths);
 927
 928     /**
 929      * @param synonymUUid
 930      * @param acceptedTaxonUuid
 931      * @return
 932      */
 933     public UpdateResult swapSynonymAndAcceptedTaxon(UUID synonymUUid, UUID acceptedTaxonUuid);
 934
 935     /**
 936      * @param taxonUuid
 937      * @param config
 938      * @param classificationUuid
 939      * @return
 940      */
 941     public DeleteResult deleteTaxon(UUID taxonUuid, TaxonDeletionConfigurator config, UUID classificationUuid);
 942
 943
 944         public UpdateResult moveFactualDateToAnotherTaxon(UUID fromTaxonUuid,
 945                         UUID toTaxonUuid);
 946
 947
 948     /**
 949      * @param synonymUuid
 950      * @param toTaxonUuid
 951      * @param taxonRelationshipType
 952      * @param citation
 953      * @param microcitation
 954      * @return
 955      */
 956     public UpdateResult changeSynonymToRelatedTaxon(UUID synonymUuid, UUID toTaxonUuid, TaxonRelationshipType taxonRelationshipType,
 957             Reference citation, String microcitation);
 958
 959     /**
 960      * @param fromTaxonUuid
 961      * @param toTaxonUuid
 962      * @param oldRelationshipType
 963      * @param synonymType
 964      * @return
 965      * @throws DataChangeNoRollbackException
 966      */
 967     public UpdateResult changeRelatedTaxonToSynonym(UUID fromTaxonUuid, UUID toTaxonUuid,
 968             TaxonRelationshipType oldRelationshipType, SynonymType synonymType) throws DataChangeNoRollbackException;
 969
 970
 971
 972
 973
 974 }