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.dto.TaxonRelationshipsDTO;
  27 import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;
  28 import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
  29 import eu.etaxonomy.cdm.api.service.pager.Pager;
  30 import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;
  31 import eu.etaxonomy.cdm.api.service.search.LuceneParseException;
  32 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  33 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  34 import eu.etaxonomy.cdm.exception.UnpublishedException;
  35 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  36 import eu.etaxonomy.cdm.model.common.Language;
  37 import eu.etaxonomy.cdm.model.common.MarkerType;
  38 import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
  39 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  40 import eu.etaxonomy.cdm.model.description.Feature;
  41 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  42 import eu.etaxonomy.cdm.model.location.NamedArea;
  43 import eu.etaxonomy.cdm.model.media.Media;
  44 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  45 import eu.etaxonomy.cdm.model.name.Rank;
  46 import eu.etaxonomy.cdm.model.name.TaxonName;
  47 import eu.etaxonomy.cdm.model.reference.Reference;
  48 import eu.etaxonomy.cdm.model.taxon.Classification;
  49 import eu.etaxonomy.cdm.model.taxon.Synonym;
  50 import eu.etaxonomy.cdm.model.taxon.SynonymType;
  51 import eu.etaxonomy.cdm.model.taxon.Taxon;
  52 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  53 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  54 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  55 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  56 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  57 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  58 import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
  59 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  60 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  61 import eu.etaxonomy.cdm.persistence.query.TaxonTitleType;
  62
  63
  64 public interface ITaxonService
  65              extends IIdentifiableEntityService<TaxonBase>, IPublishableService<TaxonBase>{
  66
  67     /**
  68      * {@inheritDoc}
  69      * <BR><BR>
  70      * NOTE: Also taxa with <code>publish=false</code> are returned.
  71      */
  72     @Override
  73     public TaxonBase load(UUID uuid, List<String> propertyPaths);
  74
  75     /**
  76      * Returns a list of taxa that matches the name string and the sec reference
  77      * @param name the name string to search for
  78      * @param sec the taxons sec reference
  79      * @return a list of taxa matching the name and the sec reference
  80      */
  81     public List<TaxonBase> searchByName(String name, boolean includeUnpublished, Reference sec);
  82
  83     /**
  84      * Swaps given synonym and accepted taxon.
  85      * In particular:
  86      * <ul>
  87      *          <li>A new accepted taxon with the synonyms name is created</li>
  88      *          <li>The synonym is deleted from the old accepted taxons synonym list</li>
  89      *          <li>A new synonym with the name of the old accepted taxon is created</li>
  90      *          <li>The newly created synonym get related to the newly created accepted taxon</li>
  91      * </ul>
  92      *
  93      * @param synonym
  94      * @param acceptedTaxon
  95      * @return
  96      */
  97     public UpdateResult swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
  98
  99     /**
 100      * Changes a synonym into an accepted taxon and removes
 101      * the synonym relationship to the given accepted taxon.
 102      * Other synonyms homotypic to the synonym to change are
 103      * moved to the same new accepted taxon as homotypic
 104      * synonyms. The new accepted taxon has the same name and
 105      * the same sec reference as the old synonym.<BR>
 106      * If the given accepted taxon and the synonym are homotypic
 107      * to each other an exception may be thrown as taxonomically it doesn't
 108      * make sense to have two accepted taxa in the same homotypic group
 109      * but also it is than difficult to decide how to handle other names
 110      * in the homotypic group. It is up to the implementing class to
 111      * handle this situation via an exception or in another way.
 112      *
 113      *
 114      * @param synonym
 115      *                          the synonym to change into an accepted taxon
 116      * @param acceptedTaxon
 117      *                          an accepted taxon, the synonym had a relationship to
 118      * @param deleteSynonym
 119      *                  if true the method tries to delete the old synonym from the database
 120      * @return
 121      *                  the newly created accepted taxon
 122      * @throws IllegalArgumentException
 123      *                  if the given accepted taxon and the synonym are homotypic
 124      *              to each other an exception may be thrown as taxonomically it doesn't
 125      *                  make sense to have two accepted taxa in the same homotypic group
 126      *          but also it is than difficult to decide how to handle other names
 127      *          in the homotypic group. It is up to the implementing class to
 128      *          handle this situation via an exception or in another way.
 129      */
 130     public UpdateResult changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym) throws HomotypicalGroupChangeException;
 131
 132     /**
 133      * @param synonymUuid
 134      * @param acceptedTaxonUuid
 135      * @param newParentNodeUuid
 136      * @param deleteSynonym
 137      * @return
 138      * @throws HomotypicalGroupChangeException
 139      */
 140     public UpdateResult changeSynonymToAcceptedTaxon(UUID synonymUuid, UUID acceptedTaxonUuid, UUID newParentNodeUuid,
 141             boolean deleteSynonym)
 142             throws HomotypicalGroupChangeException;
 143
 144     /**
 145      * Change a synonym into a related concept
 146      *
 147      * @param synonym
 148      *                          the synonym to change into the concept taxon
 149      * @param toTaxon
 150      *                          the taxon the newly created concept should be related to
 151      * @param taxonRelationshipType
 152      *                          the type of relationship
 153      * @param reference
 154      * @param microReference
 155      * @return
 156      *                          update result with the newly created concept
 157      */
 158     public UpdateResult changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference reference, String microReference);
 159
 160     /**
 161      *
 162      * Change a related concept into synonym
 163      *
 164      * @param synonym
 165      *                          the concept taxon to change into a synonym
 166      * @param toTaxon
 167      *                          the taxon the newly created synonym should be related to
 168      * @param oldRelationshipType
 169      *              the type of old concept relationship
 170      * @param synonymRelationshipType
 171      *                          the type of new synonym relationship
 172      *
 173      * @return
 174      *                          update result with the newly created synonym
 175      * @throws DataChangeNoRollbackException
 176      */
 177   public        UpdateResult changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon,
 178              TaxonRelationshipType oldRelationshipType,
 179             SynonymType synonymType) throws DataChangeNoRollbackException;
 180
 181     /**
 182      * Changes the homotypic group of a synonym into the new homotypic group.
 183      * All relations to taxa are updated correctly depending on the homotypic
 184      * group of the accepted taxon. <BR>
 185      * All existing basionym relationships to and from this name are removed.<BR>
 186      * If the parameter <code>targetTaxon</code> is defined, the synonym is
 187      * added to this taxon irrespctive of if it has been related to this
 188      * taxon before.<BR>
 189      * If <code>setBasionymRelationIfApplicable</code> is true a basionym relationship
 190      * between the existing basionym(s) of the new homotypic group and the synonyms name
 191      * is added.<BR>
 192      *
 193      * @param synonym
 194      * @param newHomotypicalGroup
 195      * @param taxon
 196      * @param setBasionymRelationIfApplicable
 197      */
 198     public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup,
 199             Taxon targetTaxon, boolean setBasionymRelationIfApplicable);
 200
 201     /**
 202      * See {@link #moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)}
 203      * @param oldSynonym
 204      * @param newTaxon
 205      * @param moveHomotypicGroup
 206      * @param newSynonymType
 207      * @return
 208      * @throws HomotypicalGroupChangeException
 209      */
 210     public UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym, Taxon newTaxon, boolean moveHomotypicGroup,
 211             SynonymType newSynonymType) throws HomotypicalGroupChangeException;
 212
 213
 214     /**
 215      * Moves a synonym to another taxon and removes the old synonym relationship.
 216      *
 217      * @param oldSynonym the old synonym to move.
 218      * @param newTaxon the taxon the synonym will be moved to
 219      * @param moveHomotypicGroup if the synonym belongs to a homotypic group with other synonyms and
 220      *          <code>moveHomotypicGroup</code> is <code>true</code> all these synonyms are moved to the new taxon,
 221      *          if <code>false</code> a {@link HomotypicalGroupChangeException} is thrown.
 222      *          <code>moveHomotypicGroup</code> has no effect if the synonym is the only synonym in it's homotypic group.
 223      * @param newSynonymType the synonym type of the new synonyms. Default is
 224      *          {@link SynonymType#HETEROTYPIC_SYNONYM_OF() heterotypic}.
 225      * @param newSecundum The secundum for the new synonyms).
 226      * @param newSecundumDetail The secundum micro reference for the new synonym(s).
 227      * @param keepSecundumIfUndefined if no <code>newSecundum</code> and/or no <code>newSecundumDetail</code>
 228      *          is defined they are taken from the old synonym(s) if <code>keepSecundumIfUndefined</code> is
 229      *          <code>true</code>. If <code>false</code> the secundum and the secundum detail will be taken
 230      *          only from the <code>newSecundum</code> and <code>newSecundumDetail</code> even if they are
 231      *      undefined (<code>null</code>).
 232      * @return The new synonym relationship. If <code>moveHomotypicGroup</code> is <code>true</code> additionally
 233      *          created new synonym relationships must be retrieved separately from the new taxon.
 234      * @throws HomotypicalGroupChangeException Exception is thrown if (1) synonym is homotypic to the old accepted taxon or
 235      *          (2) synonym is in homotypic group with other synonyms and <code>moveHomotypicGroup</code> is false
 236      */
 237     public UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym, Taxon newTaxon, boolean moveHomotypicGroup,
 238             SynonymType newSynonymType, Reference newSecundum,
 239             String newSecundumDetail, boolean keepSecundumIfUndefined) throws HomotypicalGroupChangeException;
 240
 241
 242     /**
 243      * @param oldSynonym
 244      * @param newTaxonUUID
 245      * @param moveHomotypicGroup
 246      * @param newSynonymType
 247      * @param reference
 248      * @param referenceDetail
 249      * @param keepReference
 250      * @return
 251      * @throws HomotypicalGroupChangeException
 252      *
 253      * @see {@link #moveSynonymToAnotherTaxon(Synonym, Taxon, boolean, SynonymType, Reference, String, boolean)}
 254      */
 255     public UpdateResult moveSynonymToAnotherTaxon(Synonym oldSynonym,
 256             UUID newTaxonUUID, boolean moveHomotypicGroup,
 257             SynonymType newSynonymType,
 258             Reference newSecundum, String newSecundumDetail, boolean keepSecundumIfUndefined)
 259             throws HomotypicalGroupChangeException;
 260
 261     /**
 262      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 263      * where the supplied taxon is relatedTo.
 264      *
 265      * @param taxon The taxon that is relatedTo
 266      * @param type The type of TaxonRelationship (can be null)
 267      * @param includeUnpublished should unpublished related taxa also be returned?
 268      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 269      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 270      * @param orderHints Properties to order by
 271      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 272      * @return a List of TaxonRelationship instances
 273      */
 274     public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 275             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 276
 277
 278     /**
 279      * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
 280      * where the supplied taxon is relatedTo.
 281      *
 282      * @param taxon The taxon that is relatedTo
 283      * @param type The type of TaxonRelationship (can be null)
 284      * @param includeUnpublished should unpublished related taxa also be returned?
 285      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 286      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 287      * @param orderHints Properties to order by
 288      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 289      * @return a Pager of TaxonRelationship instances
 290      */
 291     public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 292             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 293
 294     /**
 295      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 296      * where the supplied taxon is relatedFrom.
 297      *
 298      * @param taxon The taxon that is relatedFrom
 299      * @param type The type of TaxonRelationship (can be null)
 300      * @param includeUnpublished should unpublished related taxa also be returned?
 301      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 302      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 303      * @param orderHints Properties to order by
 304      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 305      * @return a List of TaxonRelationship instances
 306      */
 307     public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 308             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 309
 310
 311     /**
 312      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 313      * where the supplied taxon is relatedFrom.
 314      *
 315      * @param taxon The taxon that is relatedFrom
 316      * @param type The type of TaxonRelationship (can be null)
 317      * @param includeUnpublished should unpublished related taxa also be returned?
 318      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 319      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 320      * @param orderHints Properties to order by
 321      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 322      * @return a Pager of TaxonRelationship instances
 323      */
 324     public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 325             boolean includeUnpublished, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 326
 327     /**
 328      * lists all taxa which are related to the <code>taxon</code> given as
 329      * parameter.
 330      *
 331      * @param taxon
 332      * @param includeRelationships
 333      * @param maxDepth
 334      *            <code>1</code> for one level, <code>null</code> for infinite
 335      *            depth, <code>0</code> will completely omit collecting related taxa.
 336      * @param limit
 337      * @param start
 338      * @param propertyPaths
 339      * @return
 340      */
 341     public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,
 342             boolean includeUnpublished, Integer limit, Integer start, List<String> propertyPaths);
 343
 344
 345     /**
 346      * Returns all or a page of all taxon concept relationships in the database.
 347      * The result can be filtered by relationship types.
 348      *
 349      * @param types The taxon relationship type filter, if <code>null</code> no filter is set, if empty the result will also be empty
 350      * @param pageSize the page size
 351      * @param pageStart the number of the start page
 352      * @param orderHints the order hints
 353      * @param propertyPaths the property path to initialize the resulting objects
 354      * @return list of taxon relationships matching the filter criteria
 355      */
 356     public List<TaxonRelationship> listTaxonRelationships(Set<TaxonRelationshipType> types,
 357             Integer pageSize, Integer pageStart, List<OrderHint> orderHints, List<String> propertyPaths);
 358
 359     /**
 360      * Lists all classifications the given taxon/synonym is used in{@link Synonym}
 361      *
 362      * @param taxonBase
 363      * @param limit
 364      * @param start
 365      * @param propertyPaths
 366      * @return
 367      */
 368     public List<Classification> listClassifications(TaxonBase taxonBase, Integer limit, Integer start, List<String> propertyPaths);
 369
 370     /**
 371      * Returns the Synonyms (with the given synonym relationship type, if this argument is supplied)
 372      * that do have the supplied taxon as accepted taxon.
 373      *
 374      * @param taxon The accepted taxon
 375      * @param type The type of Synonym (can be null)
 376      * @param pageSize The maximum number of synonyms returned (can be null for returning synonyms)
 377      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 378      * * @param orderHints Properties to order by
 379      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 380      * @return a Pager of {@link Synonym} instances
 381      */
 382     public Pager<Synonym> getSynonyms(Taxon taxon, SynonymType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 383
 384     /**
 385      * This method returns in the first entry the list of synonyms of the
 386      * homotypic group of the accepted taxon. All other entries represent the lists of heterotypic
 387      * synonym groups. For detailed information about these 2 groups see
 388      * {@link #getHomotypicSynonymsByHomotypicGroup(Taxon, List)} and
 389      * {@link #getHeterotypicSynonymyGroups(Taxon, List)}
 390      *
 391      * @see                     #getSynonyms()
 392      * @see                     SynonymType#HETEROTYPIC_SYNONYM_OF()
 393      * @see                     eu.etaxonomy.cdm.model.name.HomotypicalGroup
 394
 395      * @param taxon the accepted taxon
 396      * @param propertyPaths the property path
 397      * @return the list of groups of synonyms
 398      */
 399     public List<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 400
 401
 402     /**
 403      * Returns the list of all synonyms that share the same homotypical group with the given taxon.
 404      * Only those homotypic synonyms are returned that do have a synonym relationship with the accepted taxon.
 405      * @param taxon
 406      * @param propertyPaths
 407      * @return
 408      */
 409     public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 410
 411     /**
 412      * Returns the ordered list of all {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical groups}
 413      * that contain {@link Synonym synonyms} that are heterotypic to the given taxon.
 414      * {@link eu.etaxonomy.cdm.model.name.TaxonName Taxon names} of heterotypic synonyms
 415      * belong to a homotypical group which cannot be the homotypical group to which the
 416      * taxon name of the given taxon belongs. This method does not return the homotypic group the given
 417      * taxon belongs to.<BR>
 418      * This method does neglect the type of synonym relationship that is defined between the given taxon
 419      * and the synonym. So the synonym relationship may be homotypic however a synonym is returned
 420      * in one of the result lists as long as the synonym does not belong to the same homotypic group as
 421      * the given taxon.<BR>
 422      * The list returned is ordered according to the date of publication of the
 423      * first published name within each homotypical group.
 424      *
 425      * @see                     #getHeterotypicSynonymyGroups()
 426      * @see                     #getSynonyms()
 427      * @see                     SynonymType#HETEROTYPIC_SYNONYM_OF()
 428      * @see                     eu.etaxonomy.cdm.model.name.HomotypicalGroup
 429
 430      * @param taxon
 431      * @param propertyPaths
 432      * @return
 433      */
 434     public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
 435
 436     /**
 437      * Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 438      *
 439      * @param clazz filter the results by class (or pass null to return all TaxonBase instances)
 440      * @param queryString
 441      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 442      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 443      * @param orderHints
 444      *            Supports path like <code>orderHints.propertyNames</code> which
 445      *            include *-to-one properties like createdBy.username or
 446      *            authorTeam.persistentTitleCache
 447      * @param propertyPaths properties to be initialized
 448      * @return a Pager Taxon instances
 449      * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 450      */
 451     @Override
 452     public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 453
 454     /**
 455      * Returns a list of TaxonBase instances where the
 456      * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 457      * <i>null</i> will search for those taxa with a value of null in that field
 458      *
 459      * @param clazz optionally filter by class (can be null to return all taxa)
 460      * @param uninomial
 461      * @param infragenericEpithet
 462      * @param specificEpithet
 463      * @param infraspecificEpithet
 464      * @param rank
 465      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 466      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 467      * @return a list of TaxonBase instances
 468      */
 469     public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
 470
 471     /**
 472      * Returns a list of TaxonBase instances where the
 473      * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 474      * <i>null</i> will search for those taxa with a value of null in that field
 475      *
 476      * @param clazz optionally filter by class
 477      * @param uninomial
 478      * @param infragenericEpithet
 479      * @param specificEpithet
 480      * @param infraspecificEpithet
 481      * @param rank
 482      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 483      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 484      * @return a List of TaxonBase instances
 485      */
 486     public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, String authorship, Rank rank, Integer pageSize, Integer pageNumber);
 487
 488     /**
 489      * Returns a list of IdentifiableEntity instances (in particular, TaxonName and TaxonBase instances)
 490      * that match the properties specified in the configurator.
 491      * @param configurator
 492      * @return
 493      */
 494     public Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator);
 495
 496     /**
 497      * performes a union searches for TaxonBase instances on all available
 498      * free text indexes. At the time of writing this documentation it combines
 499      * {@link #findByDescriptionElementFullText(Class, String, Classification, List, List, boolean, Integer, Integer, List, List)}
 500      * and {@link #findByFullText(Class, String, Classification, List, boolean, Integer, Integer, List, List)
 501      *
 502      * @param queryString
 503      *            the query string
 504      * @param classification
 505      *            Additional filter criterion: If a taxonomic classification
 506      *            three is specified here the result set will only contain taxa
 507      *            of the given classification
 508      * @param languages
 509      *            Additional filter criterion: Search only in these languages.
 510      *            Not all text fields in the cdm model are multilingual, thus
 511      *            this setting will only apply to the multilingiual fields.
 512      *            Other fields are searched nevertheless if this parameter is
 513      *            set or not.
 514      * @param highlightFragments
 515      *            TODO
 516      * @param pageSize
 517      *            The maximum number of objects returned (can be null for all
 518      *            objects)
 519      * @param pageNumber
 520      *            The offset (in pageSize chunks) from the start of the result
 521      *            set (0 - based)
 522      * @param orderHints
 523      *            Supports path like <code>orderHints.propertyNames</code> which
 524      *            include *-to-one properties like createdBy.username or
 525      *            authorTeam.persistentTitleCache
 526      * @param propertyPaths
 527      *            properties to initialize - see
 528      *            {@link IBeanInitializer#initialize(Object, List)}
 529      * @return a paged list of instances of type T matching the queryString and
 530      *         the additional filter criteria
 531      * @return
 532      * @throws LuceneCorruptIndexException
 533      * @throws IOException
 534      * @throws LuceneParseException
 535      * @throws LuceneMultiSearchException
 536      * @deprecated this search should fully be covered by the new method
 537      *      {@link #findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List)}
 538      *      , maybe we should rename this latter method to give it a more meaningful name
 539      */
 540     @Deprecated
 541     public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,
 542             Classification classification, TaxonNode subtree, boolean includeUnpublished, List<Language> languages, boolean highlightFragments,
 543             Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException, LuceneMultiSearchException;
 544
 545     /**
 546      * Searches for TaxonBase instances using the TaxonBase free text index.
 547      *
 548      * <h4>This is an experimental feature, it may be moved, modified, or even
 549      * removed in future releases!!!</h4>
 550      *
 551      * @param clazz
 552      *            Additional filter criterion: The specific TaxonBase subclass
 553      *            to search for
 554      * @param queryString
 555      *            the query string
 556      * @param classification
 557      *            Additional filter criterion: If a taxonomic classification
 558      *            three is specified here the result set will only contain taxa
 559      *            of the given classification
 560      * @param languages
 561      *            Additional filter criterion: Search only in these languages.
 562      *            Not all text fields in the cdm model are multilingual, thus
 563      *            this setting will only apply to the multilingiual fields.
 564      *            Other fields are searched nevertheless if this parameter is
 565      *            set or not.
 566      * @param highlightFragments
 567      *            TODO
 568      * @param pageSize
 569      *            The maximum number of objects returned (can be null for all
 570      *            objects)
 571      * @param pageNumber
 572      *            The offset (in pageSize chunks) from the start of the result
 573      *            set (0 - based)
 574      * @param orderHints
 575      *            Supports path like <code>orderHints.propertyNames</code> which
 576      *            include *-to-one properties like createdBy.username or
 577      *            authorTeam.persistentTitleCache
 578      * @param propertyPaths
 579      *            properties to initialize - see
 580      *            {@link IBeanInitializer#initialize(Object, List)}
 581      * @return a paged list of instances of type T matching the queryString and
 582      *         the additional filter criteria
 583      * @throws LuceneCorruptIndexException
 584      * @throws IOException
 585      * @throws LuceneParseException
 586      */
 587     public Pager<SearchResult<TaxonBase>> findByFullText(Class<? extends TaxonBase> clazz, String queryString,
 588             Classification classification, TaxonNode subtree,
 589             boolean includeUnpublished, List<Language> languages,
 590             boolean highlightFragments, Integer pageSize, Integer pageNumber,
 591             List<OrderHint> orderHints, List<String> propertyPaths)
 592                     throws IOException, LuceneParseException;
 593
 594
 595     /**
 596      * @param areaFilter
 597      * @param statusFilter
 598      * @param classification
 599      *            Additional filter criterion: If a taxonomic classification
 600      *            three is specified here the result set will only contain taxa
 601      *            of the given classification
 602      * @param highlightFragments
 603      * @param pageSize
 604      *            The maximum number of objects returned (can be null for all
 605      *            objects)
 606      * @param pageNumber
 607      *            The offset (in pageSize chunks) from the start of the result
 608      *            set (0 - based)
 609      * @param orderHints
 610      *            Supports path like <code>orderHints.propertyNames</code> which
 611      *            include *-to-one properties like createdBy.username or
 612      *            authorTeam.persistentTitleCache
 613      * @param propertyPath
 614      *            Common properties to initialize the instances of the
 615      *            CDM types ({@link Taxon} and {@link Synonym}
 616      *            this method can return - see {@link IBeanInitializer#initialize(Object, List)}
 617      * @return a paged list of instances of {@link Taxon} instances
 618      * @throws IOException
 619      * @throws LuceneParseException
 620      */
 621     //TODO needed? currently only used in test
 622     public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTerm> statusFilter,
 623             Classification classification, TaxonNode subtree,
 624             Integer pageSize, Integer pageNumber,
 625             List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException;
 626
 627     /**
 628      * Searches for TaxonBase instances using the TaxonBase free text index.
 629      *
 630      *
 631      *
 632      * <h4>This is an experimental feature, it may be moved, modified, or even
 633      * removed in future releases!!!</h4>
 634      * @param searchModes
 635      *            Additional filter criterion: defaults to [doTaxa] if set null
 636      * @param queryString
 637      *            the query string
 638      * @param classification
 639      *            Additional filter criterion: If a taxonomic classification
 640      *            three is specified here the result set will only contain taxa
 641      *            of the given classification
 642      * @param subtree
 643      * @param namedAreas
 644      * @param distributionStatus
 645      * @param languages
 646      *            Additional filter criterion: Search only in these languages.
 647      *            Not all text fields in the cdm model are multilingual, thus
 648      *            this setting will only apply to the multilingiual fields.
 649      *            Other fields are searched nevertheless if this parameter is
 650      *            set or not.
 651      * @param highlightFragments
 652      *            TODO
 653      * @param pageSize
 654      *            The maximum number of objects returned (can be null for all
 655      *            objects)
 656      * @param pageNumber
 657      *            The offset (in pageSize chunks) from the start of the result
 658      *            set (0 - based)
 659      * @param orderHints
 660      *            Supports path like <code>orderHints.propertyNames</code> which
 661      *            include *-to-one properties like createdBy.username or
 662      *            authorTeam.persistentTitleCache
 663      * @param propertyPath
 664      *            Common properties to initialize the instances of the
 665      *            CDM types ({@link Taxon} and {@link Synonym}
 666      *            this method can return - see {@link IBeanInitializer#initialize(Object, List)}
 667      * @return a paged list of instances of {@link Taxon}, {@link Synonym}, matching the queryString and
 668      *         the additional filter criteria
 669      * @throws LuceneCorruptIndexException
 670      * @throws IOException
 671      * @throws LuceneParseException
 672      * @throws LuceneMultiSearchException
 673      */
 674     public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(
 675             EnumSet<TaxaAndNamesSearchMode> searchModes,
 676             String queryString, Classification classification, TaxonNode subtree,
 677             Set<NamedArea> namedAreas, Set<PresenceAbsenceTerm> distributionStatus,
 678             List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 679             List<String> propertyPaths) throws IOException, LuceneParseException, LuceneMultiSearchException;
 680
 681     /**
 682      * Searches for TaxonBase instances by using the DescriptionElement free text index.
 683      *
 684      * <h4>This is an experimental feature, it may be moved, modified, or even
 685      * removed in future releases!!!</h4>
 686      *
 687      * @param clazz
 688      *            Additional filter criterion:
 689      * @param queryString
 690      *            the query string to filter by
 691      * @param classification
 692      *            Additional filter criterion: If a taxonomic classification
 693      *            tree is specified here the result set will only contain taxa
 694      *            of the given classification
 695      * @param subtree
 696      *            Additional filter criterion: If a taxonomic classification
 697      *            subtree is specified here the result set will only contain taxa
 698      *            of the given subtree
 699      * @param features
 700      *            TODO
 701      * @param languages
 702      *            Additional filter criterion: Search only in these languages.
 703      *            Not all text fields in the CDM model are multi-lingual, thus
 704      *            this setting will only apply to the multi-lingual fields.
 705      *            Other fields are searched nevertheless if this parameter is
 706      *            set or not.
 707      * @param highlightFragments
 708      *            TODO
 709      * @param pageSize
 710      *            The maximum number of objects returned (can be null for all
 711      *            objects)
 712      * @param pageNumber
 713      *            The offset (in pageSize chunks) from the start of the result
 714      *            set (0 - based)
 715      * @param orderHints
 716      *            Supports path like <code>orderHints.propertyNames</code> which
 717      *            include *-to-one properties like createdBy.username or
 718      *            authorTeam.persistentTitleCache
 719      * @param propertyPaths
 720      *            properties to initialize - see
 721      *            {@link IBeanInitializer#initialize(Object, List)}
 722      * @return a paged list of instances of type T matching the queryString and
 723      *         the additional filter criteria
 724      * @throws IOException
 725      * @throws LuceneCorruptIndexException
 726      * @throws LuceneParseException
 727      */
 728     public Pager<SearchResult<TaxonBase>> findByDescriptionElementFullText(Class<? extends DescriptionElementBase> clazz,
 729             String queryString, Classification classification, TaxonNode subtree, List<Feature> features, List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, LuceneParseException;
 730
 731     /**
 732      * Lists all Media found in an any TaxonDescription associated with this
 733      * taxon.
 734      *
 735      * @param taxon
 736      * @param includeRelationships
 737      *            the given list of TaxonRelationshipEdges will be taken into
 738      *            account when retrieving media associated with the given taxon.
 739      *            Can be NULL.
 740      * @param limitToGalleries
 741      *            whether to take only TaxonDescription into account which are
 742      *            marked as gallery
 743      * @return
 744      * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
 745      */
 746     @Deprecated
 747     public List<Media> listTaxonDescriptionMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, List<String> propertyPath);
 748
 749     /**
 750      * Lists all Media found in an any TaxonDescription, NameDescription,
 751      * SpecimenOrObservationBase, DnaSample Chromatograms, etc. associated with this taxon.
 752      *
 753      * @param taxon
 754      * @param includeRelationships
 755      *            the given list of TaxonRelationshipEdges will be taken into
 756      *            account when retrieving media associated with the given taxon.
 757      *            Can be NULL.
 758      * @param limitToGalleries
 759      *            whether to take only descriptions into account which are
 760      *            marked as gallery, can be NULL
 761      * @param includeTaxonDescriptions
 762      *            whether to take TaxonDescriptions into account, can be NULL
 763      * @param includeOccurrences
 764      *          whether to take TaxonDescriptions into account, can be NULL
 765      * @param includeTaxonNameDescriptions
 766      *       whether to take TaxonNameDescriptions into account, can be NULL
 767      * @param propertyPath
 768      * @return
 769      */
 770     public List<Media> listMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
 771             Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,
 772             Boolean includeTaxonNameDescriptions, List<String> propertyPath);
 773
 774     public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
 775
 776     /**
 777      * Returns the TaxonBase with the given UUID
 778      * using the given match mode and initialization strategy
 779      *
 780      * @param uuid
 781      * @param propertyPaths
 782      * @return
 783      */
 784     public TaxonBase findTaxonByUuid(UUID uuid, List<String> propertyPaths);
 785
 786     /**
 787      * Counts the number of synonyms
 788      * @param onlyAttachedToTaxon if <code>true</code> only those synonyms being attached to
 789      * an accepted taxon are counted
 790      * @return the number of synonyms
 791      */
 792     public long countSynonyms(boolean onlyAttachedToTaxon);
 793
 794     public List<TaxonName> findIdenticalTaxonNames(List<String> propertyPath);
 795
 796     public List<TaxonName> findIdenticalTaxonNameIds(List<String> propertyPath);
 797 //
 798 //    public String getPhylumName(TaxonName name);
 799
 800     /**
 801      * Returns all {@link Taxon taxa} which are {@link TaxonRelationshipType#CONGRUENT_TO() congruent} or
 802      * {@link TaxonRelationshipType#INCLUDES() included} in the taxon represented by the given taxon uuid.
 803      * The result also returns the path to these taxa represented by the uuids of
 804      * the {@link TaxonRelationshipType taxon relationships types} and doubtful information.
 805      * If classificationUuids is set only taxa of classifications are returned which are included
 806      * in the given {@link Classification classifications}. ALso the path to these taxa may not include
 807      * taxa from other classifications.
 808      * @param taxonUuid uuid of the original taxon
 809      * @param classificationUuids List of uuids of classifications used as a filter
 810      * @param includeDoubtful set to <code>true</code> if also doubtfully included taxa should be included in the result
 811      * @return a DTO which includes a list of taxa with the pathes from the original taxon to the given taxon as well
 812      * as doubtful and date information. The original taxon is included in the result.
 813      */
 814     public IncludedTaxaDTO listIncludedTaxa(UUID taxonUuid, IncludedTaxonConfiguration configuration);
 815
 816
 817    /**
 818      * Removes a synonym.<BR><BR>
 819      *
 820      * In detail it removes
 821      *  <li>the synonym concept</li>
 822      *  <BR><BR>
 823      *  If <code>removeNameIfPossible</code> is true
 824      *  it also removes the synonym name if it is not used in any other context
 825      *  (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)<BR><BR>
 826      *  If <code>newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name
 827      *  is not deleted and the name is homotypic to the taxon
 828      *  the name is moved to a new homotypic group.<BR><BR>
 829      *
 830      *  If synonym is <code>null</code> the method has no effect.
 831      *
 832      * @param taxon
 833      * @param synonym
 834      * @param removeNameIfPossible
 835      * @return deleteResult
 836      *
 837      */
 838     public DeleteResult deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config);
 839
 840     /**
 841      * Removes a synonym.
 842      *
 843      * The method essentially loads the synonym and calls the
 844      * {@link #deleteSynonym(Synonym, SynonymDeletionConfigurator) deleteSynonym} method
 845      *
 846      * @param synonymUuid
 847      * @param config
 848      * @return
 849      */
 850     public DeleteResult deleteSynonym(UUID synonymUuid, SynonymDeletionConfigurator config);
 851
 852     /**
 853      * @param tnb
 854      * @return
 855      */
 856     public Taxon findBestMatchingTaxon(String taxonName);
 857
 858     public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config);
 859
 860     public Synonym findBestMatchingSynonym(String taxonName, boolean includeUnpublished);
 861
 862      public List<UuidAndTitleCache<? extends IdentifiableEntity>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator);
 863
 864     /**
 865      * Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
 866      * @param taxon
 867      * @param tree
 868      * @return list of inferred synonyms
 869      */
 870     public List<Synonym> createInferredSynonyms(Taxon taxon, Classification tree, SynonymType type, boolean doWithMisappliedNames);
 871
 872     /**
 873      * Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database
 874      * @param taxon
 875      * @param tree
 876      * @param iDatabase
 877      * @return list of inferred synonyms
 878      */
 879     public List<Synonym>  createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames);
 880
 881     public Taxon findAcceptedTaxonFor(UUID synonymUuid, UUID classificationUuid, boolean includeUnpublished,
 882             List<String> propertyPaths) throws UnpublishedException;
 883
 884     public List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config);
 885
 886
 887     /**
 888      * @param clazz the optional {@link TaxonBase} subclass
 889      * @param identifier the identifier string
 890      * @param identifierType the identifier type
 891      * @param subtreeFilter filter on a classification subtree (TaxonNode)
 892      * @param matchmode the match mode for the identifier string
 893      * @param includeEntity should the taxon as an object be included in the result
 894      * @param pageSize page size
 895      * @param pageNumber page number
 896      * @param propertyPaths property path for initializing the returned taxon object (requires includeEntity=true)
 897      * @return the resulting {@link IdentifiedEntityDTO} pager
 898      * @see IIdentifiableEntityService#findByIdentifier(Class, String, DefinedTerm, MatchMode, boolean, Integer, Integer, List)
 899      */
 900     public <S extends TaxonBase> Pager<IdentifiedEntityDTO<S>> findByIdentifier(
 901                         Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,
 902                         MatchMode matchmode, boolean includeEntity, Integer pageSize,
 903                         Integer pageNumber,     List<String> propertyPaths);
 904
 905     /**
 906      * Returns a pager for {@link MarkedEntityDTO DTOs} that hold the marker including type, title and uuid
 907      * and the according {@link TaxonBase} information (uuid, title and the taxon object itself (optional)).
 908      *
 909      * @param clazz The optional {@link TaxonBase} subclass
 910      * @param markerType the obligatory marker type, if not given, the results will always be empty
 911      * @param markerValue the optional
 912      * @param subtreeFilter filter on a classification subtree (TaxonNode)
 913      * @param includeEntity should the taxon as an object be included in the result
 914      * @param titleType which label to give the returned entity, taxon.titleCache, name.titleCache or name.nameCache
 915      * @param pageSize page size
 916      * @param pageNumber page number
 917      * @param propertyPaths property path for initializing the returned taxon object (requires includeEntity=true)
 918      * @return the resulting {@link MarkedEntityDTO} pager
 919      * @see IIdentifiableEntityService#findByMarker(Class, MarkerType, Boolean, boolean, Integer, Integer, List)
 920      */
 921     public <S extends TaxonBase> Pager<MarkedEntityDTO<S>> findByMarker(
 922             Class<S> clazz, MarkerType markerType, Boolean markerValue,
 923             TaxonNode subtreeFilter, boolean includeEntity, TaxonTitleType titleType,
 924             Integer pageSize, Integer pageNumber, List<String> propertyPaths);
 925
 926     /**
 927      * @param synonymUUid
 928      * @param acceptedTaxonUuid
 929      * @return
 930      */
 931     public UpdateResult swapSynonymAndAcceptedTaxon(UUID synonymUUid, UUID acceptedTaxonUuid);
 932
 933     /**
 934      * @param taxonUuid
 935      * @param config
 936      * @param classificationUuid
 937      * @return
 938      */
 939     public DeleteResult deleteTaxon(UUID taxonUuid, TaxonDeletionConfigurator config, UUID classificationUuid);
 940
 941
 942         public UpdateResult moveFactualDateToAnotherTaxon(UUID fromTaxonUuid,
 943                         UUID toTaxonUuid);
 944
 945
 946     /**
 947      * @param synonymUuid
 948      * @param toTaxonUuid
 949      * @param taxonRelationshipType
 950      * @param citation
 951      * @param microcitation
 952      * @return
 953      */
 954     public UpdateResult changeSynonymToRelatedTaxon(UUID synonymUuid, UUID toTaxonUuid, TaxonRelationshipType taxonRelationshipType,
 955             Reference citation, String microcitation);
 956
 957     /**
 958      * @param fromTaxonUuid
 959      * @param toTaxonUuid
 960      * @param oldRelationshipType
 961      * @param synonymType
 962      * @return
 963      * @throws DataChangeNoRollbackException
 964      */
 965     public UpdateResult changeRelatedTaxonToSynonym(UUID fromTaxonUuid, UUID toTaxonUuid,
 966             TaxonRelationshipType oldRelationshipType, SynonymType synonymType) throws DataChangeNoRollbackException;
 967
 968     /**
 969      * Returns a list of taxon relationships for a given taxon as DTO.
 970      * @param taxonUuid
 971      * @param directTypes
 972      * @param inversTypes
 973      * @param direction
 974      * @param groupMisapplications
 975      * @param includeUnpublished
 976      * @param pageSize
 977      * @param pageNumber
 978      * @return
 979      */
 980     public TaxonRelationshipsDTO listTaxonRelationships(UUID taxonUuid,
 981             Set<TaxonRelationshipType> directTypes,
 982             Set<TaxonRelationshipType> inversTypes, Direction direction, boolean groupMisapplications,
 983             boolean includeUnpublished, Integer pageSize, Integer pageNumber);
 984
 985
 986
 987
 988 }