cdmlib-services/src/main/java/eu/etaxonomy/cdm/api/service/INameService.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.Collection;
  15 import java.util.List;
  16 import java.util.Map;
  17 import java.util.UUID;
  18
  19 import org.apache.lucene.index.CorruptIndexException;
  20 import org.apache.lucene.queryParser.ParseException;
  21 import org.hibernate.criterion.Criterion;
  22
  23 import eu.etaxonomy.cdm.api.service.config.NameDeletionConfigurator;
  24 import eu.etaxonomy.cdm.api.service.exception.ReferencedObjectUndeletableException;
  25 import eu.etaxonomy.cdm.api.service.pager.Pager;
  26 import eu.etaxonomy.cdm.api.service.search.DocumentSearchResult;
  27 import eu.etaxonomy.cdm.api.service.search.SearchResult;
  28 import eu.etaxonomy.cdm.model.common.CdmBase;
  29 import eu.etaxonomy.cdm.model.common.Language;
  30 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  31 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  32 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  33 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  34 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  35 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  36 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  37 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  38 import eu.etaxonomy.cdm.model.name.NameRelationship;
  39 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  40 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  41 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  42 import eu.etaxonomy.cdm.model.name.NonViralName;
  43 import eu.etaxonomy.cdm.model.name.Rank;
  44 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  45 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  46 import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
  47 import eu.etaxonomy.cdm.persistence.dao.IBeanInitializer;
  48 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  49 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  50 import eu.etaxonomy.cdm.strategy.cache.TaggedText;
  51
  52 public interface INameService extends IIdentifiableEntityService<TaxonNameBase> {
  53
  54         /**
  55          * Deletes a name. Depening on the configurator state links to the name will either be
  56          * deleted or throw exceptions.<BR>
  57          * If name is <code>null</code> this method has no effect.
  58          * @param name
  59          * @param config
  60          * @throws ReferencedObjectUndeletableException
  61          */
  62         public UUID delete(TaxonNameBase name, NameDeletionConfigurator config) throws ReferencedObjectUndeletableException;
  63
  64         /**
  65          * Removes the given type designation from the given taxon name and deletes it from
  66          * the database if it is not connected to any other name.
  67          * If <code>typeDesignation</code> is <code>null</code> all type designations are deleted
  68          * from the given taxon name. If <code>name</code> is <code>null</code> all names are removed from
  69          * the given type designation. If both are <code>null</code> nothing happens.
  70          * @param typeDesignation
  71          * @param name
  72          * @return
  73          */
  74         public void deleteTypeDesignation(TaxonNameBase name, TypeDesignationBase typeDesignation);
  75
  76
  77         /**
  78          * Saves the given type designations.
  79          * @param typeDesignationCollection
  80          * @return
  81          */
  82         public Map<UUID, TypeDesignationBase> saveTypeDesignationAll(Collection<TypeDesignationBase> typeDesignationCollection);
  83
  84         public Map<UUID, ReferencedEntityBase> saveReferencedEntitiesAll(Collection<ReferencedEntityBase> referencedEntityCollection);
  85
  86         /**
  87          * Saves the given homotypical groups.
  88          * @param homotypicalGroups
  89          * @return
  90          */
  91         public Map<UUID, HomotypicalGroup> saveAllHomotypicalGroups(Collection<HomotypicalGroup> homotypicalGroups);
  92
  93         /**
  94          * Returns all nomenclatural status.
  95          * @param limit
  96          * @param start
  97          * @return
  98          */
  99         public List<NomenclaturalStatus> getAllNomenclaturalStatus(int limit, int start);
 100
 101         /**
 102          * Returns all type designations.
 103          * @param limit
 104          * @param start
 105          * @return
 106          */
 107         public List<TypeDesignationBase> getAllTypeDesignations(int limit, int start);
 108
 109         /**
 110          * @param name
 111          * @return
 112          */
 113         public List<TaxonNameBase> getNamesByName(String name);
 114
 115         /**
 116          * Returns all NonViralNames with a name cache that matches the given string
 117          * @param name
 118          * @return
 119          */
 120         public List<NonViralName> getNamesByNameCache(String nameCache);
 121
 122         /**
 123          * Returns all NonViralNames with a title cache that matches the given string
 124          * using the given match mode and initialization strategy
 125          *
 126          * @param name
 127          * @param matchMode
 128          * @param propertyPaths
 129          * @return
 130          */
 131         public List<NonViralName> findNamesByTitleCache(String titleCache, MatchMode matchMode, List<String> propertyPaths);
 132
 133         /**
 134          * Returns all NonViralNames with a name cache that matches the given string
 135          * using the given match mode and initialization strategy
 136          *
 137          * @param name
 138          * @param matchMode
 139          * @param propertyPaths
 140          * @return
 141          */
 142         public List<NonViralName> findNamesByNameCache(String nameCache, MatchMode matchMode, List<String> propertyPaths);
 143
 144         /**
 145          * Returns the NonViralName with the given UUID
 146          * using the given match mode and initialization strategy
 147          *
 148          * @param uuid
 149          * @param propertyPaths
 150          * @return
 151          */
 152         public NonViralName findNameByUuid(UUID uuid, List<String> propertyPaths);
 153         /**
 154          * @param name
 155          * @param sessionObject An object that is attached to the session before executing the query
 156          * @return
 157          */
 158         public List getNamesByName(String name, CdmBase sessionObject);
 159
 160         /**
 161          * Fuzzy matching for the taxon name elements. The input name is first atomised using the {@link NonViralNameParserImpl}
 162          * into its separate parts (genusOrUninomial,infraGenericEpithet,specificEpithet,infraGenericEpithet,authorshipCache).
 163          * Each field is then matched separately with the same accuracy parameter.
 164          *
 165          * @param name taxon name to fuzzy match
 166          * @param accuracy value > 0.0 and < 1.0 which determines the accuracy of the result.
 167          * @param languages list of languages to consider when matching (currently not used)
 168          * @param highlightFragments
 169          * @param propertyPaths
 170          * @param maxNoOfResults
 171          * @return
 172          * @throws CorruptIndexException
 173          * @throws IOException
 174          * @throws ParseException
 175          */
 176         public List<SearchResult<TaxonNameBase>> findByNameFuzzySearch(
 177             String name,
 178             float accuracy,
 179             List<Language> languages,
 180             boolean highlightFragments,
 181             List<String> propertyPaths,
 182             int maxNoOfResults) throws CorruptIndexException, IOException, ParseException;
 183
 184         /**
 185          * Fuzzy matching for the taxon name elements using only the lucene index.
 186          *
 187          * The input name is first atomised using the {@link NonViralNameParserImpl}
 188          * into its separate parts (genusOrUninomial,infraGenericEpithet,specificEpithet,infraGenericEpithet,authorshipCache).
 189          * Each field is then matched separately with the same accuracy parameter.
 190          *
 191          * @param name taxon name to fuzzy match
 192          * @param accuracy value > 0.0 and < 1.0 which determines the accuracy of the result.
 193          * @param languages list of languages to consider when matching (currently not used)
 194          * @param highlightFragments
 195          * @param maxNoOfResults
 196          * @return
 197          * @throws CorruptIndexException
 198          * @throws IOException
 199          * @throws ParseException
 200          */
 201     public List<DocumentSearchResult> findByNameFuzzySearch(
 202             String name,
 203             float accuracy,
 204             List<Language> languages,
 205             boolean highlightFragments,
 206             int maxNoOfResults) throws CorruptIndexException, IOException, ParseException;
 207
 208         /**
 209          * Exact matching for the taxon name elements using only the lucene index.
 210          *
 211          * The input name is first atomised using the {@link NonViralNameParserImpl}
 212          * into its separate parts (genusOrUninomial,infraGenericEpithet,specificEpithet,infraGenericEpithet,authorshipCache).
 213          * Each field is then matched separately with the same accuracy parameter.
 214          *
 215          * @param name taxon name to fuzzy match
 216          * @param wildcard boolean flag to indicate whether a wildcard '*' should be added at the end of the query
 217          * @param languages list of languages to consider when matching (currently not used)
 218          * @param highlightFragments
 219          * @param maxNoOfResults
 220          * @return
 221          * @throws CorruptIndexException
 222          * @throws IOException
 223          * @throws ParseException
 224          */
 225
 226     public List<DocumentSearchResult> findByNameExactSearch(
 227             String name,
 228             boolean wildcard,
 229             List<Language> languages,
 230             boolean highlightFragments,
 231             int maxNoOfResults) throws CorruptIndexException, IOException, ParseException;
 232
 233         // TODO: Remove getNamesByName() methods. Use findNamesByTitle() instead.
 234
 235         // FIXME candidate for harmonization?
 236         public List findNamesByTitle(String title);
 237
 238         public List findNamesByTitle(String title, CdmBase sessionObject);
 239
 240     public List<HomotypicalGroup> getAllHomotypicalGroups(int limit, int start);
 241
 242         @Deprecated
 243     public List<RelationshipBase> getAllRelationships(int limit, int start);
 244
 245         /**
 246          * Returns all Ranks
 247          * @return
 248          * @deprecated use VocabularyService#getVocabulary(VocabularyEnum) instead,
 249          *   this is not possible since  VocabularyService#getVocabulary(VocabularyEnum)
 250          *   is not returning a OrderedTermVocabulary !!! see also http://dev.e-taxonomy.eu/trac/ticket/3327
 251          */
 252         @Deprecated
 253     public OrderedTermVocabulary<Rank> getRankVocabulary();
 254
 255         /**
 256          * Returns all NomenclaturalStatusTypes
 257          * @return
 258          * @deprecated use VocabularyService#getVocabulary(VocabularyEnum) instead
 259          */
 260         @Deprecated
 261     public TermVocabulary<NomenclaturalStatusType> getStatusTypeVocabulary();
 262
 263         /**
 264          * Returns TypeDesignationStatus vocabulary
 265          * @return
 266          * @deprecated use VocabularyService#getVocabulary(VocabularyEnum) instead
 267          */
 268         @Deprecated
 269     public TermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationStatusVocabulary();
 270
 271         /**
 272          * Returns TypeDesignationStatus ordered vocabulary
 273          * @return
 274          * @deprecated use VocabularyService#getVocabulary(VocabularyEnum) instead
 275          */
 276         @Deprecated
 277     public OrderedTermVocabulary<SpecimenTypeDesignationStatus> getSpecimenTypeDesignationVocabulary();
 278
 279         /**
 280          * Returns all NameRelationshipTypes
 281          * @return
 282          * @deprecated use VocabularyService#getVocabulary(VocabularyEnum) instead
 283          */
 284         @Deprecated
 285     public TermVocabulary<NameRelationshipType> getNameRelationshipTypeVocabulary();
 286
 287         /**
 288          * Return a List of name relationships in which this name is related to
 289          * another name, optionally filtered by relationship type
 290          *
 291          * @param name
 292          *            the name on either the <i>"from side"</i> or on the
 293          *            <i>"to side"</i> of the relationship, depending on the
 294          *            <code>direction</code> of the relationship.
 295          * @param direction
 296          *            the direction of the NameRelationship, may be null to return all relationships
 297          * @param type
 298          *            the relationship type (or null to return all relationships)
 299          * @param pageSize
 300          *            The maximum number of relationships returned (can be null for
 301          *            all relationships)
 302          * @param pageNumber
 303          *            The offset (in pageSize chunks) from the start of the result
 304          *            set (0 - based)
 305          * @param orderHints
 306          *            may be null
 307          * @param propertyPaths
 308          *            properties to initialize - see
 309          *            {@link IBeanInitializer#initialize(Object, List)}
 310          * @return a Pager of NameRelationship instances
 311          */
 312         public List<NameRelationship> listNameRelationships(TaxonNameBase name,  NameRelationship.Direction direction, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 313
 314         /**
 315          * Return a List of name relationships in which this name is related to another name, optionally filtered
 316          * by relationship type
 317          *
 318          * @param name the name on the <i>"from side"</i> of the relationship
 319          * @param direction the direction of the NameRelationship
 320          * @param type the relationship type (or null to return all relationships)
 321          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 322          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 323          * @param orderHints may be null
 324          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 325          * @return a Pager of NameRelationship instances
 326          */
 327         public Pager<NameRelationship> pageNameRelationships(TaxonNameBase name,  NameRelationship.Direction direction, NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 328
 329         /**
 330          * Return a List of relationships in which this name is related to another name, optionally filtered
 331          * by relationship type
 332          *
 333          * @param name the name on the <i>"from side"</i> of the relationship
 334          * @param type the relationship type (or null to return all relationships)
 335          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 336          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 337          * @param orderHints may be null
 338          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 339          * @return a Pager of NameRelationship instances
 340          * @deprecated use {@link #listNameRelationships(TaxonNameBase, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
 341          */
 342         @Deprecated
 343         public List<NameRelationship> listFromNameRelationships(TaxonNameBase name,  NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 344
 345         /**
 346          * Return a List of relationships in which this name is related to another name, optionally filtered
 347          * by relationship type
 348          *
 349          * @param name the name on the <i>"from side"</i> of the relationship
 350          * @param type the relationship type (or null to return all relationships)
 351          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 352          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 353          * @param orderHints may be null
 354          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 355          * @return a Pager of NameRelationship instances
 356          * @deprecated use {@link #pageNameRelationships(TaxonNameBase, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
 357          */
 358         @Deprecated
 359         public Pager<NameRelationship> pageFromNameRelationships(TaxonNameBase name,  NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 360
 361         /**
 362          * Return a List of relationships in which another name is related to this name, optionally filtered
 363          * by relationship type
 364          *
 365          * @param name the name on the <i>"to side"</i> of the relationship
 366          * @param type the relationship type (or null to return all relationships)
 367          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 368          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 369          * @param orderHints may be null
 370          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 371          * @return a Pager of NameRelationship instances
 372          * @deprecated use {@link #listNameRelationships(TaxonNameBase, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
 373          */
 374         @Deprecated
 375         public List<NameRelationship> listToNameRelationships(TaxonNameBase name,  NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 376
 377         /**
 378          * Return a List of relationships in which another name is related to this name, optionally filtered
 379          * by relationship type
 380          *
 381          * @param name the name on the <i>"to side"</i> of the relationship
 382          * @param type the relationship type (or null to return all relationships)
 383          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 384          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 385          * @param orderHints may be null
 386          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 387          * @return a Pager of NameRelationship instances
 388          * @deprecated use {@link #pageNameRelationships(TaxonNameBase, eu.etaxonomy.cdm.model.common.RelationshipBase.Direction, NameRelationshipType, Integer, Integer, List, List)} instead
 389          */
 390         @Deprecated
 391         public Pager<NameRelationship> pageToNameRelationships(TaxonNameBase name,  NameRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 392
 393
 394         /**
 395          * Return a List of hybrids related to this name, optionally filtered
 396          * by hybrid relationship type
 397          *
 398          * @param name the name
 399          * @param type the hybrid relationship type (or null to return all hybrids)
 400          * @param pageSize The maximum number of hybrid 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 may be null
 403          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 404          * @return a Pager of HybridRelationship instances
 405          */
 406         public Pager<HybridRelationship> getHybridNames(NonViralName name, HybridRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 407
 408         /**
 409          * Return a List of types related to this name, optionally filtered
 410          * by type designation status
 411          *
 412          * @param name the name
 413          * @param status the type designation status (or null to return all types)
 414          * @param pageSize The maximum number of types returned (can be null for all types)
 415          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 416          * @return a Pager of TypeDesignationBase instances
 417          */
 418         public Pager<TypeDesignationBase> getTypeDesignations(TaxonNameBase name,
 419                         SpecimenTypeDesignationStatus status, Integer pageSize, Integer pageNumber);
 420
 421         public Pager<TypeDesignationBase> getTypeDesignations(TaxonNameBase name,
 422                         SpecimenTypeDesignationStatus status, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
 423
 424
 425         /**
 426          * Returns a List of TaxonNameBase instances that match the properties passed
 427          *
 428          * @param uninomial
 429          * @param infraGenericEpithet
 430          * @param specificEpithet
 431          * @param infraspecificEpithet
 432          * @param rank
 433          * @param pageSize The maximum number of names returned (can be null for all names)
 434          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 435          * @param orderHints may be null
 436          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 437          * @return a Pager of TaxonNameBase instances
 438          */
 439         public Pager<TaxonNameBase> searchNames(String uninomial, String infraGenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 440
 441         /**
 442          * Returns a Paged List of TaxonNameBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 443          *
 444          * @param clazz filter the results by class (or pass null to return all TaxonNameBase instances)
 445          * @param queryString
 446          * @param pageSize The maximum number of names returned (can be null for all matching names)
 447          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 448          * @param orderHints
 449          *            Supports path like <code>orderHints.propertyNames</code> which
 450          *            include *-to-one properties like createdBy.username or
 451          *            authorTeam.persistentTitleCache
 452          * @param propertyPaths properties to be initialized
 453          * @return a Pager TaxonNameBase instances
 454          * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 455          */
 456         @Override
 457     public Pager<TaxonNameBase> search(Class<? extends TaxonNameBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 458
 459         /**
 460          * Returns a map that holds uuid, titleCache pairs of all names in the current database
 461          *
 462          * @return
 463          *                      a <code>Map</code> containing uuid and titleCache of names
 464          */
 465         public List<UuidAndTitleCache> getUuidAndTitleCacheOfNames();
 466
 467         /**
 468          * Return a Pager of names matching the given query string, optionally filtered by class, optionally with a particular MatchMode
 469          *
 470          * @param clazz filter by class - can be null to include all instances of type T
 471          * @param queryString the query string to filter by
 472          * @param matchmode use a particular type of matching (can be null - defaults to exact matching)
 473          * @param criteria additional criteria to filter by
 474          * @param pageSize The maximum number of objects returned (can be null for all objects)
 475          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 476          * @param propertyPaths properties to initialize - see {@link IBeanInitializer#initialize(Object, List)}
 477          * @param orderHints
 478          *            Supports path like <code>orderHints.propertyNames</code> which
 479          *            include *-to-one properties like createdBy.username or
 480          *            authorTeam.persistentTitleCache
 481          * @return a paged list of instances of type T matching the queryString
 482          */
 483     public Pager<TaxonNameBase> findByName(Class<? extends TaxonNameBase> clazz, String queryString,MatchMode matchmode, List<Criterion> criteria, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 484
 485     /**
 486      * Returns a homotypical group with the given UUID or null if not homotypical group exists with that UUID
 487      *
 488      * @param uuid the uuid of the homotypical group
 489      * @return a homotypical group
 490      */
 491     public HomotypicalGroup findHomotypicalGroup(UUID uuid);
 492
 493     /**
 494      * @param uuid
 495      * @return
 496      */
 497     public List<TaggedText> getTaggedName(UUID uuid);
 498 }