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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.io.IOException;
  14 import java.util.EnumSet;
  15 import java.util.List;
  16 import java.util.Set;
  17 import java.util.UUID;
  18
  19 import org.apache.lucene.index.CorruptIndexException;
  20 import org.apache.lucene.queryParser.ParseException;
  21 import org.springframework.transaction.annotation.Transactional;
  22
  23 import eu.etaxonomy.cdm.api.service.config.IFindTaxaAndNamesConfigurator;
  24 import eu.etaxonomy.cdm.api.service.config.IncludedTaxonConfiguration;
  25 import eu.etaxonomy.cdm.api.service.config.MatchingTaxonConfigurator;
  26 import eu.etaxonomy.cdm.api.service.config.SynonymDeletionConfigurator;
  27 import eu.etaxonomy.cdm.api.service.config.TaxonDeletionConfigurator;
  28 import eu.etaxonomy.cdm.api.service.dto.FindByIdentifierDTO;
  29 import eu.etaxonomy.cdm.api.service.dto.IncludedTaxaDTO;
  30 import eu.etaxonomy.cdm.api.service.exception.DataChangeNoRollbackException;
  31 import eu.etaxonomy.cdm.api.service.exception.HomotypicalGroupChangeException;
  32 import eu.etaxonomy.cdm.api.service.pager.Pager;
  33 import eu.etaxonomy.cdm.api.service.search.LuceneMultiSearchException;
  34 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  35 import eu.etaxonomy.cdm.api.service.util.TaxonRelationshipEdge;
  36 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  37 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  38 import eu.etaxonomy.cdm.model.common.Language;
  39 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  40 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  41 import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
  42 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  43 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  44 import eu.etaxonomy.cdm.model.description.Feature;
  45 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  46 import eu.etaxonomy.cdm.model.location.NamedArea;
  47 import eu.etaxonomy.cdm.model.media.Media;
  48 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  49 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  50 import eu.etaxonomy.cdm.model.name.Rank;
  51 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  52 import eu.etaxonomy.cdm.model.reference.Reference;
  53 import eu.etaxonomy.cdm.model.taxon.Classification;
  54 import eu.etaxonomy.cdm.model.taxon.Synonym;
  55 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  56 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  57 import eu.etaxonomy.cdm.model.taxon.Taxon;
  58 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  59 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  60 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  61 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  62 import eu.etaxonomy.cdm.persistence.dao.initializer.IBeanInitializer;
  63 import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
  64 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  65 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  66
  67
  68 public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
  69
  70     /**
  71      * Computes all Taxon instances that do not have a taxonomic parent.
  72      * @param sec The concept reference that the taxon belongs to
  73      *
  74      * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  75      * @return The List<Taxon> of root taxa.
  76      * @deprecated obsolete when using classification
  77      */
  78     @Deprecated
  79     public List<Taxon> getRootTaxa(Reference sec, CdmFetch cdmFetch, boolean onlyWithChildren);
  80
  81     /**
  82      * Computes all Taxon instances which name is of a certain Rank.
  83      * @param rank The rank of the taxon name
  84      * @param sec The concept reference that the taxon belongs to
  85      * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  86      * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  87      * the misapplied name are not returned.<Br>Default: true.
  88      * @param propertyPaths
  89      *            properties to be initialized, For detailed description and
  90      *            examples <b>please refer to:</b>
  91      *            {@link IBeanInitializer#initialize(Object, List)}. <Br>
  92      *            Default: true.
  93      * @return The List<Taxon> of root taxa.
  94      * @deprecated obsolete when using classification
  95      */
  96     @Deprecated
  97     public List<Taxon> getRootTaxa(Rank rank, Reference sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
  98
  99     /**
 100      * Computes all relationships.
 101      * @param limit
 102      * @param start
 103      * @return
 104      * FIXME candidate for harmonization - rename to listRelationships
 105      */
 106     public List<RelationshipBase> getAllRelationships(int limit, int start);
 107
 108     /**
 109      * Returns TaxonRelationshipType vocabulary
 110      * @return
 111      * @deprecated use TermService#getVocabulary(VocabularyType) instead
 112      */
 113     @Deprecated
 114     public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
 115
 116     /**
 117      * Returns a list of taxa that matches the name string and the sec reference
 118      * @param name the name string to search for
 119      * @param sec the taxons sec reference
 120      * @return a list of taxa matching the name and the sec reference
 121      */
 122     public List<TaxonBase> searchTaxaByName(String name, Reference sec);
 123
 124     /**
 125      * Swaps given synonym and accepted taxon.
 126      * In particular:
 127      * <ul>
 128      *          <li>A new accepted taxon with the synonyms name is created</li>
 129      *          <li>The synonym is deleted from the old accepted taxons synonym list</li>
 130      *          <li>A new synonym with the name of the old accepted taxon is created</li>
 131      *          <li>The newly created synonym get related to the newly created accepted taxon</li>
 132      * </ul>
 133      *
 134      * @param synonym
 135      * @param acceptedTaxon
 136      * @param synonymRelationshipType the relationship type the newly created synonym will have. Defaults to SYNONYM_OF
 137      */
 138     public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 139
 140     /**
 141      * Changes a synonym into an accepted taxon and removes
 142      * the synonym relationship to the given accepted taxon.
 143      * Other synonyms homotypic to the synonym to change are
 144      * moved to the same new accepted taxon as homotypic
 145      * synonyms. The new accepted taxon has the same name and
 146      * the same sec reference as the old synonym.<BR>
 147      * If the given accepted taxon and the synonym are homotypic
 148      * to each other an exception may be thrown as taxonomically it doesn't
 149      * make sense to have two accepted taxa in the same homotypic group
 150      * but also it is than difficult to decide how to handle other names
 151      * in the homotypic group. It is up to the implementing class to
 152      * handle this situation via an exception or in another way.
 153      *
 154      *
 155      * @param synonym
 156      *                          the synonym to change into an accepted taxon
 157      * @param acceptedTaxon
 158      *                          an accepted taxon, the synonym had a relationship to
 159      * @param deleteSynonym
 160      *                  if true the method tries to delete the old synonym from the database
 161      * @param copyCitationInfo
 162      *                  if true the citation and the microcitation of newly created synonyms
 163      *                  is taken from the old synonym relationships.
 164      * @param citation
 165      *                  if given this citation is added to the newly created synonym
 166      *                  relationships as citation. Only used if copyCitationInfo is <code> false</code>
 167      * @param microCitation
 168      *                  if given this microCitation is added to the newly created synonym
 169      *                  relationships as microCitation.Only used if copyCitationInfo is <code> false</code>
 170      * @return
 171      *                  the newly created accepted taxon
 172      * @throws IllegalArgumentException
 173      *                  if the given accepted taxon and the synonym are homotypic
 174      *              to each other an exception may be thrown as taxonomically it doesn't
 175      *                  make sense to have two accepted taxa in the same homotypic group
 176      *          but also it is than difficult to decide how to handle other names
 177      *          in the homotypic group. It is up to the implementing class to
 178      *          handle this situation via an exception or in another way.
 179      */
 180     public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon, boolean deleteSynonym, boolean copyCitationInfo, Reference citation, String microCitation) throws HomotypicalGroupChangeException;
 181
 182     /**
 183      * TODO still needed and correct?
 184      * Change a synonym into a related concept
 185      *
 186      * @param synonym
 187      *                          the synonym to change into the concept taxon
 188      * @param toTaxon
 189      *                          the taxon the newly created concept should be related to
 190      * @param taxonRelationshipType
 191      *                          the type of relationship
 192      * @param reference
 193      * @param microReference
 194      * @return
 195      *                          the newly created concept
 196      */
 197     public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, Reference reference, String microReference);
 198
 199     /**
 200      * TODO still needed and correct?
 201      * Change a synonym into a related concept
 202      *
 203      * @param synonym
 204      *                          the synonym to change into the concept taxon
 205      * @param toTaxon
 206      *                          the taxon the newly created concept should be related to
 207      * @param taxonRelationshipType
 208      *                          the type of relationship
 209      * @param reference
 210      * @param microReference
 211      * @return
 212      *                          the newly created concept
 213      * @throws DataChangeNoRollbackException
 214      */
 215   public        Synonym changeRelatedTaxonToSynonym(Taxon fromTaxon, Taxon toTaxon,
 216              TaxonRelationshipType oldRelationshipType,
 217             SynonymRelationshipType synonymRelationshipType) throws DataChangeNoRollbackException;
 218     /**
 219      * Deletes all synonym relationships of a given synonym. If taxon is given
 220      * only those relationships to the taxon are deleted.
 221      *
 222      * @param syn
 223      *            the synonym
 224      * @param taxon
 225      * @return
 226      * @deprecated This method must no longer being used since the
 227      *             SynonymRelationship is annotated at the {@link Taxon} and at
 228      *             the {@link Synonym} with <code>orphanDelete=true</code>. Just
 229      *             remove the from and to entities from the relationship and
 230      *             hibernate will care for the deletion. Using this method can cause
 231      *             <code>StaleStateException</code> (see http://dev.e-taxonomy.eu/trac/ticket/3797)
 232      *
 233      */
 234     @Deprecated
 235     public long deleteSynonymRelationships(Synonym syn, Taxon taxon);
 236
 237     /**
 238      * Deletes a taxon from the underlying database according to the given {@link TaxonDeletionConfigurator configurator}.
 239      * @param taxon
 240      * @param config
 241      *
 242      */
 243     public DeleteResult deleteTaxon(Taxon taxon, TaxonDeletionConfigurator config, Classification classification) ;
 244
 245     /**
 246      * Changes the homotypic group of a synonym into the new homotypic group.
 247      * All relations to taxa are updated correctly depending on the homotypic
 248      * group of the accepted taxon. <BR>
 249      * All existing basionym relationships to and from this name are removed.<BR>
 250      * If the parameter <code>targetTaxon</code> is defined, the synonym is
 251      * added to this taxon irrespctive of if it has been related to this
 252      * taxon before.<BR>
 253      * If <code>removeFromOtherTaxa</code> is true and <code>targetTaxon</code> is
 254      * defined all relationships to other taxa are deleted.<BR>
 255      * If <code>setBasionymRelationIfApplicable</code> is true a basionym relationship
 256      * between the existing basionym(s) of the new homotypic group and the synonyms name
 257      * is added.<BR>
 258      *
 259      * @param synonym
 260      * @param newHomotypicalGroup
 261      * @param taxon
 262      * @param setBasionymRelationIfApplicable
 263      */
 264     public void changeHomotypicalGroupOfSynonym(Synonym synonym, HomotypicalGroup newHomotypicalGroup, Taxon targetTaxon,
 265                         boolean removeFromOtherTaxa, boolean setBasionymRelationIfApplicable);
 266
 267
 268     /**
 269      * Moves a synonym to another taxon and removes the old synonym relationship.
 270      *
 271      * @param oldSynonymRelation the old synonym relationship defining the synonym to move and the old accepted taxon.
 272      * @param newTaxon the taxon the synonym will be moved to
 273      * @param moveHomotypicGroup if the synonym belongs to a homotypical group with other synonyms and
 274      *          <code>moveHomotypicGroup</code> is <code>true</code> all these synonyms are moved to the new taxon,
 275      *          if <code>false</code> a {@link HomotypicalGroupChangeException} is thrown.
 276      *          <code>MoveHomotypicGroup</code> has no effect if the synonym is the only synonym in it's homotypic group.
 277      * @param newSynonymRelationshipType the synonym relationship type of the new synonym relations. Default is
 278      *          {@link SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF() heterotypic}.
 279      * @param newReference The reference for the new synonym relation(s).
 280      * @param newReferenceDetail The reference detail for the new synonym relation(s).
 281      * @param keepReference if no <code>newReference</code> and/or no <code>newReferenceDetail</code>
 282      *          is defined they are taken from the old synonym relation(s) if <code>keepReference</code> is
 283      *          <code>true</code>. If <code>false</code> the reference and the reference detail will be taken
 284      *          only from the <code>newReference</code> and <code>newReferenceDetail</code>.
 285      * @return The new synonym relationship. If <code>moveHomotypicGroup</code> is <code>true</code> additionally
 286      *          created new synonym relationships must be retrieved separately from the new taxon.
 287      * @throws HomotypicalGroupChangeException Exception is thrown if (1) synonym is homotypic to the old accepted taxon or
 288      *          (2) synonym is in homotypic group with other synonyms and <code>moveHomotypicGroup</code> is false
 289      */
 290     public SynonymRelationship moveSynonymToAnotherTaxon(SynonymRelationship oldSynonymRelation, Taxon newTaxon, boolean moveHomotypicGroup,
 291             SynonymRelationshipType newSynonymRelationshipType, Reference newReference, String newReferenceDetail, boolean keepReference) throws HomotypicalGroupChangeException;
 292
 293     /**
 294      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 295      * where the supplied taxon is relatedTo.
 296      *
 297      * @param taxon The taxon that is relatedTo
 298      * @param type The type of TaxonRelationship (can be null)
 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> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 306
 307
 308
 309     /**
 310      * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
 311      * where the supplied taxon is relatedTo.
 312      *
 313      * @param taxon The taxon that is relatedTo
 314      * @param type The type of TaxonRelationship (can be null)
 315      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 316      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 317      * @param orderHints Properties to order by
 318      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 319      * @return a Pager of TaxonRelationship instances
 320      */
 321     public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 322
 323     /**
 324      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 325      * where the supplied taxon is relatedFrom.
 326      *
 327      * @param taxon The taxon that is relatedFrom
 328      * @param type The type of TaxonRelationship (can be null)
 329      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 330      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 331      * @param orderHints Properties to order by
 332      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 333      * @return a List of TaxonRelationship instances
 334      */
 335     public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 336
 337
 338     /**
 339      * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 340      * where the supplied taxon is relatedFrom.
 341      *
 342      * @param taxon The taxon that is relatedFrom
 343      * @param type The type of TaxonRelationship (can be null)
 344      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 345      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 346      * @param orderHints Properties to order by
 347      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 348      * @return a Pager of TaxonRelationship instances
 349      */
 350     public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 351
 352     /**
 353      * lists all taxa which are related to the <code>taxon</code> given as
 354      * parameter.
 355      *
 356      * @param taxon
 357      * @param includeRelationships
 358      * @param maxDepth
 359      *            <code>1</code> for one level, <code>null</code> for infinite
 360      *            depth, <code>0</code> will completely omit collecting related taxa.
 361      * @param limit
 362      * @param start
 363      * @param propertyPaths
 364      * @return
 365      */
 366     public Set<Taxon> listRelatedTaxa(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, Integer maxDepth,
 367             Integer limit, Integer start, List<String> propertyPaths);
 368
 369     /**
 370      * lists all accepted taxa for the given {@link Synonym}
 371      *
 372      * @param taxonBase
 373      * @param limit
 374      * @param start
 375      * @param propertyPaths
 376      * @return
 377      */
 378     public List<Classification> listClassifications(TaxonBase taxonBase, Integer limit, Integer start, List<String> propertyPaths);
 379
 380     /**
 381      * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 382      * where the supplied synonym is relatedFrom.
 383      *
 384      * @param taxon The synonym that is relatedFrom
 385      * @param type The type of SynonymRelationship (can be null)
 386      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 387      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 388      * * @param orderHints Properties to order by
 389      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 390      * @return a Pager of SynonymRelationship instances
 391      */
 392     public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 393
 394     /**
 395      * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 396      * where the supplied taxon is relatedTo.
 397      *
 398      * @param taxon The taxon that is relatedTo
 399      * @param type The type of SynonymRelationship (can be null)
 400      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 401      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 402      * * @param orderHints Properties to order by
 403      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 404      * @return a Pager of SynonymRelationship instances
 405      */
 406     public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 407
 408     /**
 409      * This method returns in the first entry the list of synonyms of the
 410      * homotypic group of the accepted taxon. All other entries represent the lists of heterotypic
 411      * synonym groups. For detailed information about these 2 groups see
 412      * {@link #getHomotypicSynonymsByHomotypicGroup(Taxon, List)} and
 413      * {@link #getHeterotypicSynonymyGroups(Taxon, List)}
 414      *
 415      * @see                     #getSynonyms()
 416      * @see                     SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF()
 417      * @see                     eu.etaxonomy.cdm.model.name.HomotypicalGroup
 418
 419      * @param taxon the accepted taxon
 420      * @param propertyPaths the property path
 421      * @return the list of groups of synonyms
 422      */
 423     public List<List<Synonym>> getSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 424
 425
 426     /**
 427      * Returns the list of all synonyms that share the same homotypical group with the given taxon.
 428      * Only those homotypic synonyms are returned that do have a synonym relationship with the accepted taxon.
 429      * @param taxon
 430      * @param propertyPaths
 431      * @return
 432      */
 433     public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 434
 435     /**
 436      * Returns the ordered list of all {@link eu.etaxonomy.cdm.model.name.HomotypicalGroup homotypical groups}
 437      * that contain {@link Synonym synonyms} that are heterotypic to the given taxon.
 438      * {@link eu.etaxonomy.cdm.model.name.TaxonNameBase Taxon names} of heterotypic synonyms
 439      * belong to a homotypical group which cannot be the homotypical group to which the
 440      * taxon name of the given taxon belongs. This method does not return the homotypic group the given
 441      * taxon belongs to.<BR>
 442      * This method does neglect the type of synonym relationship that is defined between the given taxon
 443      * and the synonym. So the synonym relationship may be homotypic however a synonym is returned
 444      * in one of the result lists as long as the synonym does not belong to the same homotypic group as
 445      * the given taxon.<BR>
 446      * The list returned is ordered according to the date of publication of the
 447      * first published name within each homotypical group.
 448      *
 449      * @see                     #getHeterotypicSynonymyGroups()
 450      * @see                     #getSynonyms()
 451      * @see                     SynonymRelationshipType#HETEROTYPIC_SYNONYM_OF()
 452      * @see                     eu.etaxonomy.cdm.model.name.HomotypicalGroup
 453
 454      * @param taxon
 455      * @param propertyPaths
 456      * @return
 457      */
 458     public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
 459
 460     /**
 461      * Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 462      *
 463      * @param clazz filter the results by class (or pass null to return all TaxonBase instances)
 464      * @param queryString
 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      * @param orderHints
 468      *            Supports path like <code>orderHints.propertyNames</code> which
 469      *            include *-to-one properties like createdBy.username or
 470      *            authorTeam.persistentTitleCache
 471      * @param propertyPaths properties to be initialized
 472      * @return a Pager Taxon instances
 473      * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 474      */
 475     @Override
 476     public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 477
 478     /**
 479      * Returns a list of TaxonBase instances where the
 480      * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 481      * <i>null</i> will search for those taxa with a value of null in that field
 482      *
 483      * @param clazz optionally filter by class (can be null to return all taxa)
 484      * @param uninomial
 485      * @param infragenericEpithet
 486      * @param specificEpithet
 487      * @param infraspecificEpithet
 488      * @param rank
 489      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 490      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 491      * @return a list of TaxonBase instances
 492      */
 493     public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 494
 495     /**
 496      * Returns a list of TaxonBase instances where the
 497      * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 498      * <i>null</i> will search for those taxa with a value of null in that field
 499      *
 500      * @param clazz optionally filter by class
 501      * @param uninomial
 502      * @param infragenericEpithet
 503      * @param specificEpithet
 504      * @param infraspecificEpithet
 505      * @param rank
 506      * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 507      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 508      * @return a List of TaxonBase instances
 509      */
 510     public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 511
 512     /**
 513      * Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)
 514      * that match the properties specified in the configurator.
 515      * @param configurator
 516      * @return
 517      */
 518     public Pager<IdentifiableEntity> findTaxaAndNames(IFindTaxaAndNamesConfigurator configurator);
 519
 520     /**
 521      * performes a union searches for TaxonBase instances on all available
 522      * free text indexes. At the time of writing this documentation it combines
 523      * {@link #findByDescriptionElementFullText(Class, String, Classification, List, List, boolean, Integer, Integer, List, List)}
 524      * and {@link #findByFullText(Class, String, Classification, List, boolean, Integer, Integer, List, List)
 525      *
 526      * @param queryString
 527      *            the query string
 528      * @param classification
 529      *            Additional filter criterion: If a taxonomic classification
 530      *            three is specified here the result set will only contain taxa
 531      *            of the given classification
 532      * @param languages
 533      *            Additional filter criterion: Search only in these languages.
 534      *            Not all text fields in the cdm model are multilingual, thus
 535      *            this setting will only apply to the multilingiual fields.
 536      *            Other fields are searched nevertheless if this parameter is
 537      *            set or not.
 538      * @param highlightFragments
 539      *            TODO
 540      * @param pageSize
 541      *            The maximum number of objects returned (can be null for all
 542      *            objects)
 543      * @param pageNumber
 544      *            The offset (in pageSize chunks) from the start of the result
 545      *            set (0 - based)
 546      * @param orderHints
 547      *            Supports path like <code>orderHints.propertyNames</code> which
 548      *            include *-to-one properties like createdBy.username or
 549      *            authorTeam.persistentTitleCache
 550      * @param propertyPaths
 551      *            properties to initialize - see
 552      *            {@link IBeanInitializer#initialize(Object, List)}
 553      * @return a paged list of instances of type T matching the queryString and
 554      *         the additional filter criteria
 555      * @return
 556      * @throws CorruptIndexException
 557      * @throws IOException
 558      * @throws ParseException
 559      * @throws LuceneMultiSearchException
 560      * @deprecated this search should fully be covered by the new method
 561      *      {@link #findTaxaAndNamesByFullText(EnumSet, String, Classification, Set, List, boolean, Integer, Integer, List, List)}
 562      *      , maybe we should rename this latter method to give it a more meaningful name
 563      */
 564     @Deprecated
 565     public Pager<SearchResult<TaxonBase>> findByEverythingFullText(String queryString,
 566             Classification classification, List<Language> languages, boolean highlightFragments,
 567             Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException;
 568
 569     /**
 570      * Searches for TaxonBase instances using the TaxonBase free text index.
 571      *
 572      * <h4>This is an experimental feature, it may be moved, modified, or even
 573      * removed in future releases!!!</h4>
 574      *
 575      * @param clazz
 576      *            Additional filter criterion: The specific TaxonBase subclass
 577      *            to search for
 578      * @param queryString
 579      *            the query string
 580      * @param classification
 581      *            Additional filter criterion: If a taxonomic classification
 582      *            three is specified here the result set will only contain taxa
 583      *            of the given classification
 584      * @param languages
 585      *            Additional filter criterion: Search only in these languages.
 586      *            Not all text fields in the cdm model are multilingual, thus
 587      *            this setting will only apply to the multilingiual fields.
 588      *            Other fields are searched nevertheless if this parameter is
 589      *            set or not.
 590      * @param highlightFragments
 591      *            TODO
 592      * @param pageSize
 593      *            The maximum number of objects returned (can be null for all
 594      *            objects)
 595      * @param pageNumber
 596      *            The offset (in pageSize chunks) from the start of the result
 597      *            set (0 - based)
 598      * @param orderHints
 599      *            Supports path like <code>orderHints.propertyNames</code> which
 600      *            include *-to-one properties like createdBy.username or
 601      *            authorTeam.persistentTitleCache
 602      * @param propertyPaths
 603      *            properties to initialize - see
 604      *            {@link IBeanInitializer#initialize(Object, List)}
 605      * @return a paged list of instances of type T matching the queryString and
 606      *         the additional filter criteria
 607      * @throws CorruptIndexException
 608      * @throws IOException
 609      * @throws ParseException
 610      */
 611     public Pager<SearchResult<TaxonBase>> findByFullText(Class<? extends TaxonBase> clazz, String queryString, Classification classification,
 612             List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 613             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException;
 614
 615
 616     /**
 617      * @param areaFilter
 618      * @param statusFilter
 619      * @param classification
 620      *            Additional filter criterion: If a taxonomic classification
 621      *            three is specified here the result set will only contain taxa
 622      *            of the given classification
 623      * @param highlightFragments
 624      * @param pageSize
 625      *            The maximum number of objects returned (can be null for all
 626      *            objects)
 627      * @param pageNumber
 628      *            The offset (in pageSize chunks) from the start of the result
 629      *            set (0 - based)
 630      * @param orderHints
 631      *            Supports path like <code>orderHints.propertyNames</code> which
 632      *            include *-to-one properties like createdBy.username or
 633      *            authorTeam.persistentTitleCache
 634      * @param propertyPath
 635      *            Common properties to initialize the instances of the
 636      *            CDM types ({@link Taxon} and {@link Synonym}
 637      *            this method can return - see {@link IBeanInitializer#initialize(Object, List)}
 638      * @return a paged list of instances of {@link Taxon} instances
 639      * @throws IOException
 640      * @throws ParseException
 641      */
 642     public Pager<SearchResult<TaxonBase>> findByDistribution(List<NamedArea> areaFilter, List<PresenceAbsenceTerm> statusFilter,
 643             Classification classification,
 644             Integer pageSize, Integer pageNumber,
 645             List<OrderHint> orderHints, List<String> propertyPaths) throws IOException, ParseException;
 646
 647     /**
 648      * Searches for TaxonBase instances using the TaxonBase free text index.
 649      *
 650      *
 651      *
 652      * <h4>This is an experimental feature, it may be moved, modified, or even
 653      * removed in future releases!!!</h4>
 654      * @param searchModes
 655      *            Additional filter criterion: defaults to [doTaxa] if set null
 656      * @param queryString
 657      *            the query string
 658      * @param classification
 659      *            Additional filter criterion: If a taxonomic classification
 660      *            three is specified here the result set will only contain taxa
 661      *            of the given classification
 662      * @param namedAreas
 663      * @param languages
 664      *            Additional filter criterion: Search only in these languages.
 665      *            Not all text fields in the cdm model are multilingual, thus
 666      *            this setting will only apply to the multilingiual fields.
 667      *            Other fields are searched nevertheless if this parameter is
 668      *            set or not.
 669      * @param highlightFragments
 670      *            TODO
 671      * @param pageSize
 672      *            The maximum number of objects returned (can be null for all
 673      *            objects)
 674      * @param pageNumber
 675      *            The offset (in pageSize chunks) from the start of the result
 676      *            set (0 - based)
 677      * @param orderHints
 678      *            Supports path like <code>orderHints.propertyNames</code> which
 679      *            include *-to-one properties like createdBy.username or
 680      *            authorTeam.persistentTitleCache
 681      * @param propertyPath
 682      *            Common properties to initialize the instances of the
 683      *            CDM types ({@link Taxon} and {@link Synonym}
 684      *            this method can return - see {@link IBeanInitializer#initialize(Object, List)}
 685      * @return a paged list of instances of {@link Taxon}, {@link Synonym}, matching the queryString and
 686      *         the additional filter criteria
 687      * @throws CorruptIndexException
 688      * @throws IOException
 689      * @throws ParseException
 690      * @throws LuceneMultiSearchException
 691      */
 692     public Pager<SearchResult<TaxonBase>> findTaxaAndNamesByFullText(
 693             EnumSet<TaxaAndNamesSearchMode> searchModes,
 694             String queryString, Classification classification, Set<NamedArea> namedAreas, Set<PresenceAbsenceTerm> distributionStatus,
 695             List<Language> languages, boolean highlightFragments, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 696             List<String> propertyPaths) throws CorruptIndexException, IOException, ParseException, LuceneMultiSearchException;
 697
 698     /**
 699      * Searches for TaxonBase instances by using the DescriptionElement free text index.
 700      *
 701      * <h4>This is an experimental feature, it may be moved, modified, or even
 702      * removed in future releases!!!</h4>
 703      *
 704      * @param clazz
 705      *            Additional filter criterion:
 706      * @param queryString
 707      *            the query string to filter by
 708      * @param classification
 709      *            Additional filter criterion: If a taxonomic classification
 710      *            three is specified here the result set will only contain taxa
 711      *            of the given classification
 712      * @param features
 713      *            TODO
 714      * @param languages
 715      *            Additional filter criterion: Search only in these languages.
 716      *            Not all text fields in the cdm model are multilingual, thus
 717      *            this setting will only apply to the multilingiual fields.
 718      *            Other fields are searched nevertheless if this parameter is
 719      *            set or not.
 720      * @param highlightFragments
 721      *            TODO
 722      * @param pageSize
 723      *            The maximum number of objects returned (can be null for all
 724      *            objects)
 725      * @param pageNumber
 726      *            The offset (in pageSize chunks) from the start of the result
 727      *            set (0 - based)
 728      * @param orderHints
 729      *            Supports path like <code>orderHints.propertyNames</code> which
 730      *            include *-to-one properties like createdBy.username or
 731      *            authorTeam.persistentTitleCache
 732      * @param propertyPaths
 733      *            properties to initialize - see
 734      *            {@link IBeanInitializer#initialize(Object, List)}
 735      * @return a paged list of instances of type T matching the queryString and
 736      *         the additional filter criteria
 737      * @throws IOException
 738      * @throws CorruptIndexException
 739      * @throws ParseException
 740      */
 741     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 CorruptIndexException, IOException, ParseException;
 742
 743
 744     /**
 745      *
 746      * @param taxon
 747      * @param size
 748      * @param height
 749      * @param widthOrDuration
 750      * @param mimeTypes
 751      * @return
 752      *
 753      * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
 754      */
 755     @Deprecated
 756     public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
 757
 758
 759     /**
 760      * Lists all Media found in an any TaxonDescription associated with this
 761      * taxon.
 762      *
 763      * @param taxon
 764      * @param includeRelationships
 765      *            the given list of TaxonRelationshipEdges will be taken into
 766      *            account when retrieving media associated with the given taxon.
 767      *            Can be NULL.
 768      * @param limitToGalleries
 769      *            whether to take only TaxonDescription into account which are
 770      *            marked as gallery
 771      * @return
 772      * @deprecated use {@link #listMedia(Taxon, Set, boolean, boolean, List)} instead
 773      */
 774     @Deprecated
 775     public List<Media> listTaxonDescriptionMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships, boolean limitToGalleries, List<String> propertyPath);
 776
 777     /**
 778      * Lists all Media found in an any TaxonDescription, NameDescription,
 779      * SpecimenOrObservationBase, DnaSample Chromatograms, etc. associated with this taxon.
 780      *
 781      * @param taxon
 782      * @param includeRelationships
 783      *            the given list of TaxonRelationshipEdges will be taken into
 784      *            account when retrieving media associated with the given taxon.
 785      *            Can be NULL.
 786      * @param limitToGalleries
 787      *            whether to take only descriptions into account which are
 788      *            marked as gallery, can be NULL
 789      * @param includeTaxonDescriptions
 790      *            whether to take TaxonDescriptions into account, can be NULL
 791      * @param includeOccurrences
 792      *          whether to take TaxonDescriptions into account, can be NULL
 793      * @param includeTaxonNameDescriptions
 794      *       whether to take TaxonNameDescriptions into account, can be NULL
 795      * @param propertyPath
 796      * @return
 797      */
 798     public List<Media> listMedia(Taxon taxon, Set<TaxonRelationshipEdge> includeRelationships,
 799             Boolean limitToGalleries, Boolean includeTaxonDescriptions, Boolean includeOccurrences,
 800             Boolean includeTaxonNameDescriptions, List<String> propertyPath);
 801
 802     public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
 803
 804     /**
 805      * Returns the TaxonBase with the given UUID
 806      * using the given match mode and initialization strategy
 807      *
 808      * @param uuid
 809      * @param propertyPaths
 810      * @return
 811      */
 812     public TaxonBase findTaxonByUuid(UUID uuid, List<String> propertyPaths);
 813
 814     public int countAllRelationships();
 815
 816     public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
 817
 818     public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath);
 819
 820     public String getPhylumName(TaxonNameBase name);
 821
 822     public long deleteSynonymRelationships(Synonym syn);
 823
 824     /**
 825      * Returns all {@link Taxon taxa} which are {@link TaxonRelationshipType#CONGRUENT_TO() congruent} or
 826      * {@link TaxonRelationshipType#INCLUDES() included} in the taxon represented by the given taxon uuid.
 827      * The result also returns the path to these taxa represented by the uuids of
 828      * the {@link TaxonRelationshipType taxon relationships types} and doubtful information.
 829      * If classificationUuids is set only taxa of classifications are returned which are included
 830      * in the given {@link Classification classifications}. ALso the path to these taxa may not include
 831      * taxa from other classifications.
 832      * @param taxonUuid uuid of the original taxon
 833      * @param classificationUuids List of uuids of classifications used as a filter
 834      * @param includeDoubtful set to <code>true</code> if also doubtfully included taxa should be included in the result
 835      * @return a DTO which includes a list of taxa with the pathes from the original taxon to the given taxon as well
 836      * as doubtful and date information. The original taxon is included in the result.
 837      */
 838     public IncludedTaxaDTO listIncludedTaxa(UUID taxonUuid, IncludedTaxonConfiguration configuration);
 839
 840
 841    /**
 842      * Removes a synonym.<BR><BR>
 843      *
 844      * In detail it removes
 845      *  <li>all synonym relationship to the given taxon or to all taxa if taxon is <code>null</code></li>
 846      *  <li>the synonym concept if it is not referenced by any synonym relationship anymore</li>
 847      *  <BR><BR>
 848      *  If <code>removeNameIfPossible</code> is true
 849      *  it also removes the synonym name if it is not used in any other context
 850      *  (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)<BR><BR>
 851      *  If <code>newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name is not deleted and
 852      *  the name is homotypic to the taxon the name is moved to a new homotypical group.<BR><BR>
 853      *
 854      *  If synonym is <code>null</code> the method has no effect.
 855      *
 856      * @param taxon
 857      * @param synonym
 858      * @param removeNameIfPossible
 859      * @return deleteResult
 860      *
 861      */
 862     public DeleteResult deleteSynonym(Synonym synonym, SynonymDeletionConfigurator config);
 863
 864
 865     /**
 866      * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 867      * depending on direction, where the supplied taxon is relatedTo or the supplied synonym is relatedFrom.
 868      *
 869      * @param taxonBase The taxon or synonym that is relatedTo or relatedFrom
 870      * @param type The type of SynonymRelationship (can be null)
 871      * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 872      * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 873      * @param orderHints Properties to order by
 874      * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link IBeanInitializer#initialize(Object, List)}
 875      * @param direction The direction of the relationship
 876      * @return a List of SynonymRelationship instances
 877      */
 878     public List<SynonymRelationship> listSynonymRelationships(
 879             TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
 880             List<OrderHint> orderHints, List<String> propertyPaths, Direction direction);
 881
 882     /**
 883      * @param tnb
 884      * @return
 885      */
 886     public Taxon findBestMatchingTaxon(String taxonName);
 887
 888     public Taxon findBestMatchingTaxon(MatchingTaxonConfigurator config);
 889
 890     public Synonym findBestMatchingSynonym(String taxonName);
 891
 892     public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheTaxon();
 893
 894     public List<UuidAndTitleCache<TaxonBase>> getUuidAndTitleCacheSynonym();
 895
 896     public List<UuidAndTitleCache<IdentifiableEntity>> findTaxaAndNamesForEditor(IFindTaxaAndNamesConfigurator configurator);
 897
 898     /**
 899      * Creates the specified inferred synonyms for the taxon in the classification, but do not insert it to the database
 900      * @param taxon
 901      * @param tree
 902      * @return list of inferred synonyms
 903      */
 904     public List<Synonym> createInferredSynonyms(Taxon taxon, Classification tree, SynonymRelationshipType type, boolean doWithMisappliedNames);
 905
 906     /**
 907      * Creates all inferred synonyms for the taxon in the classification, but do not insert it to the database
 908      * @param taxon
 909      * @param tree
 910      * @param iDatabase
 911      * @return list of inferred synonyms
 912      */
 913     public List<Synonym>  createAllInferredSynonyms(Taxon taxon, Classification tree, boolean doWithMisappliedNames);
 914
 915
 916
 917
 918     /**
 919      * Removes a synonym.<BR><BR>
 920      *
 921      * In detail it removes
 922      *  <li>all synonym relationship to the given taxon or to all taxa if taxon is <code>null</code></li>
 923      *  <li>the synonym concept if it is not referenced by any synonym relationship anymore</li>
 924      *  <BR><BR>
 925      *  If <code>config.removeNameIfPossible</code> is true
 926      *  it also removes the synonym name if it is not used in any other context
 927      *  (part of a concept, in DescriptionElementSource, part of a name relationship, used inline, ...)<BR><BR>
 928      *  If <code>config.newHomotypicGroupIfNeeded</code> is <code>true</code> and the synonym name is not deleted and
 929      *  the name is homotypic to the taxon the name is moved to a new homotypical group.<BR><BR>
 930      *
 931      *  If synonym is <code>null</code> the method has no effect.
 932      *
 933      * @param taxon
 934      * @param synonym
 935      * @param config
 936      * @return deleteResult
 937      */
 938     DeleteResult deleteSynonym(Synonym synonym, Taxon taxon,
 939             SynonymDeletionConfigurator config);
 940
 941     public Pager<Taxon> pageAcceptedTaxaFor(UUID synonymUuid, UUID classificationUuid, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 942             List<String> propertyPaths);
 943
 944     public List<Taxon> listAcceptedTaxaFor(UUID synonymUuid, UUID classificationUuid, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints,
 945             List<String> propertyPaths);
 946
 947     public List<TaxonBase> findTaxaByName(MatchingTaxonConfigurator config);
 948
 949
 950     public <S extends TaxonBase> Pager<FindByIdentifierDTO<S>> findByIdentifier(
 951                         Class<S> clazz, String identifier, DefinedTerm identifierType, TaxonNode subtreeFilter,
 952                         MatchMode matchmode, boolean includeEntity, Integer pageSize,
 953                         Integer pageNumber,     List<String> propertyPaths);
 954
 955
 956
 957
 958 }