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

   1 // $Id$
   2 /**
   3 * Copyright (C) 2007 EDIT
   4 * European Distributed Institute of Taxonomy
   5 * http://www.e-taxonomy.eu
   6 *
   7 * The contents of this file are subject to the Mozilla Public License Version 1.1
   8 * See LICENSE.TXT at the top of this package for the full license terms.
   9 */
  10
  11 package eu.etaxonomy.cdm.api.service;
  12
  13 import java.util.List;
  14 import java.util.Set;
  15
  16 import eu.etaxonomy.cdm.api.service.config.ITaxonServiceConfigurator;
  17 import eu.etaxonomy.cdm.api.service.pager.Pager;
  18 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  19 import eu.etaxonomy.cdm.model.common.OrderedTermVocabulary;
  20 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  21 import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
  22 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  23 import eu.etaxonomy.cdm.model.name.NonViralName;
  24 import eu.etaxonomy.cdm.model.name.Rank;
  25 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  26 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  27 import eu.etaxonomy.cdm.model.taxon.Synonym;
  28 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  29 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  30 import eu.etaxonomy.cdm.model.taxon.Taxon;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  35 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  36 import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
  37 import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
  38 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  39
  40
  41 public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
  42
  43         /**
  44          * Computes all taxon bases.
  45          * FIXME could substitute with list(Synonym.class, limit, start)
  46          * @param limit
  47          * @param start
  48          * @return
  49          */
  50         public List<Synonym> getAllSynonyms(int limit, int start);
  51
  52         /**
  53          * Computes all taxon bases.
  54          * FIXME could substitute with list(Taxon.class, limit,start)
  55          * @param limit
  56          * @param start
  57          * @return
  58          */
  59         public List<Taxon> getAllTaxa(int limit, int start);
  60
  61         /**
  62          * Computes all Taxon instances that do not have a taxonomic parent and has at least one child.
  63          * @param sec The concept reference that the taxon belongs to
  64          * @return The List<Taxon> of root taxa.
  65          * @deprecated obsolete when using taxonomicTree
  66          */
  67         public List<Taxon> getRootTaxa(ReferenceBase sec);
  68
  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 taxonomicTree
  77          */
  78         public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren);
  79
  80         /**
  81          * Computes all Taxon instances that do not have a taxonomic parent.
  82          * @param sec The concept reference that the taxon belongs to
  83          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  84          * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  85          * the misapplied name are not returned.<Br>Default: true.
  86          * @return The List<Taxon> of root taxa.
  87          * @deprecated obsolete when using taxonomicTree
  88          */
  89         public List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications);
  90
  91         /**
  92          * Computes all Taxon instances which name is of a certain Rank.
  93          * @param rank The rank of the taxon name
  94          * @param sec The concept reference that the taxon belongs to
  95          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  96          * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  97          * the misapplied name are not returned.<Br>Default: true.
  98          * @param propertyPaths
  99          *            properties to be initialized, For detailed description and
 100          *            examples <b>please refer to:</b>
 101          *            {@link BeanInitializer#initialize(Object, List)}. <Br>
 102          *            Default: true.
 103          * @return The List<Taxon> of root taxa.
 104          * @deprecated obsolete when using taxonomicTree
 105          */
 106         public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
 107
 108         /**
 109          * Computes all relationships.
 110          * @param limit
 111          * @param start
 112          * @return
 113          */
 114     public List<RelationshipBase> getAllRelationships(int limit, int start);
 115
 116         /**
 117          * Returns TaxonRelationshipType vocabulary
 118          * @return
 119          * @deprecated use TermService#getVocabulary(VocabularyType) instead
 120          */
 121         public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
 122
 123         /**
 124          * Returns a list of taxa that matches the name string and the sec reference
 125          * @param name the name string to search for
 126          * @param sec the taxons sec reference
 127          * @return a list of taxa matching the name and the sec reference
 128          */
 129         public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec);
 130
 131         /**
 132          * Changes an accepted taxon to a synonym of another taxon.
 133          *
 134          * @param oldTaxonNode
 135          *                              the <code>TaxonNode</code> of the accepted taxon that will be changed into a synonym
 136          * @param newAcceptedTaxonNode
 137          *                              the <code>TaxonNode</code> of the accepted taxon, the old taxon will become a synonym of
 138          * @param synonymType
 139          *                              <code>SynonymRelationshipType</code> to indicate whether hetero or homotypic
 140          * @param citation
 141          *                              the reference for this assumption
 142          * @param citationMicroReference
 143          *                              the micro citation
 144          * @return
 145          *                              the newly created synonym
 146          */
 147         public Synonym changeAcceptedTaxonToSynonym (TaxonNode oldTaxonNode, TaxonNode newAcceptedTaxonNode, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference);
 148
 149         /**
 150          * Swaps given synonym and accepted taxon.
 151          * In particular:
 152          * <ul>
 153          *              <li>A new accepted taxon with the synonyms name is created</li>
 154          *              <li>The synonym is deleted from the old accepted taxons synonym list</li>
 155          *              <li>A new synonym with the name of the old accepted taxon is created</li>
 156          *              <li>The newly created synonym get related to the newly created accepted taxon</li>
 157          * </ul>
 158          *
 159          * @param synonym
 160          * @param acceptedTaxon
 161          * @param synonymRelationshipType the relationship type the newly created synonym will have. Defaults to SYNONYM_OF
 162          */
 163         public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 164
 165         /**
 166          * Change a synonym into an accepted taxon and removes
 167          * the synonym relationship to the given accepted taxon.
 168          *
 169          * @param synonym
 170          *                              the synonym to change into an accepted taxon
 171          * @param acceptedTaxon
 172          *                              an accepted taxon, the synonym had a relationship to
 173          * @return
 174          *                              the newly created accepted taxon
 175          */
 176         public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 177
 178         /**
 179          * Change a synonym into a related concept
 180          *
 181          * @param synonym
 182          *                              the synonym to change into the concept taxon
 183          * @param toTaxon
 184          *                              the taxon the newly created concept should be related to
 185          * @param taxonRelationshipType
 186          *                              the type of relationship
 187          * @param citation
 188          * @param microcitation
 189          * @return
 190          *                              the newly created concept
 191          */
 192         public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, ReferenceBase citation, String microcitation);
 193
 194         /**
 195          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 196          * where the supplied taxon is relatedTo.
 197          *
 198          * @param taxon The taxon that is relatedTo
 199          * @param type The type of TaxonRelationship (can be null)
 200          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 201          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 202          * @param orderHints Properties to order by
 203          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 204          * @return a List of TaxonRelationship instances
 205          */
 206         public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 207
 208
 209
 210         /**
 211          * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
 212          * where the supplied taxon is relatedTo.
 213          *
 214          * @param taxon The taxon that is relatedTo
 215          * @param type The type of TaxonRelationship (can be null)
 216          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 217          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 218          * @param orderHints Properties to order by
 219          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 220          * @return a Pager of TaxonRelationship instances
 221          */
 222         public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 223
 224         /**
 225          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 226          * where the supplied taxon is relatedFrom.
 227          *
 228          * @param taxon The taxon that is relatedFrom
 229          * @param type The type of TaxonRelationship (can be null)
 230          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 231          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 232          * @param orderHints Properties to order by
 233          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 234          * @return a List of TaxonRelationship instances
 235          */
 236         public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 237
 238
 239         /**
 240          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 241          * where the supplied taxon is relatedFrom.
 242          *
 243          * @param taxon The taxon that is relatedFrom
 244          * @param type The type of TaxonRelationship (can be null)
 245          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 246          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 247          * @param orderHints Properties to order by
 248          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 249          * @return a Pager of TaxonRelationship instances
 250          */
 251         public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 252
 253         /**
 254          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 255          * where the supplied synonym is relatedFrom.
 256          *
 257          * @param taxon The synonym that is relatedFrom
 258          * @param type The type of SynonymRelationship (can be null)
 259          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 260          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 261          * * @param orderHints Properties to order by
 262          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 263          * @return a Pager of SynonymRelationship instances
 264          */
 265         public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 266
 267         /**
 268          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 269          * where the supplied taxon is relatedTo.
 270          *
 271          * @param taxon The taxon that is relatedTo
 272          * @param type The type of SynonymRelationship (can be null)
 273          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 274          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 275          * * @param orderHints Properties to order by
 276          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 277          * @return a Pager of SynonymRelationship instances
 278          */
 279         public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 280
 281         public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 282
 283         public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
 284
 285         /**
 286          * Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 287          *
 288          * @param clazz filter the results by class (or pass null to return all TaxonBase instances)
 289          * @param queryString
 290          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 291          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 292          * @param orderHints
 293          *            Supports path like <code>orderHints.propertyNames</code> which
 294          *            include *-to-one properties like createdBy.username or
 295          *            authorTeam.persistentTitleCache
 296          * @param propertyPaths properties to be initialized
 297          * @return a Pager Taxon instances
 298          * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 299          */
 300         public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 301
 302         /**
 303          * Returns a list of TaxonBase instances where the
 304          * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 305          * <i>null</i> will search for those taxa with a value of null in that field
 306          *
 307          * @param clazz optionally filter by class (can be null to return all taxa)
 308          * @param uninomial
 309          * @param infragenericEpithet
 310          * @param specificEpithet
 311          * @param infraspecificEpithet
 312          * @param rank
 313          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 314          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 315          * @return a list of TaxonBase instances
 316          */
 317         public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 318
 319         /**
 320          * Returns a list of TaxonBase instances where the
 321          * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 322          * <i>null</i> will search for those taxa with a value of null in that field
 323          *
 324          * @param clazz optionally filter by class
 325          * @param uninomial
 326          * @param infragenericEpithet
 327          * @param specificEpithet
 328          * @param infraspecificEpithet
 329          * @param rank
 330          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 331          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 332          * @return a List of TaxonBase instances
 333          */
 334         public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 335
 336         /**
 337          * Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)
 338          * that match the properties specified in the configurator.
 339          * @param configurator
 340          * @return
 341          */
 342         public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator);
 343
 344         /**
 345          *
 346          * @param taxon
 347          * @param size
 348          * @param height
 349          * @param widthOrDuration
 350          * @param mimeTypes
 351          * @return
 352          */
 353         public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
 354
 355         public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
 356         /**
 357          * returns a list of inferred synonyms concerning the taxon with synonymrelationshiptype type
 358          * @param tree
 359          * @param taxon
 360          * @param type
 361          * @return
 362          */
 363         public List<Synonym> createInferredSynonyms(TaxonomicTree tree, Taxon taxon, SynonymRelationshipType type);
 364         /**
 365          * returns a list of all inferred synonyms (inferred epithet, inferred genus and potential combination) concerning the taxon
 366          * @param tree
 367          * @param taxon
 368          * @return
 369          */
 370         public List<Synonym> createAllInferredSynonyms(TaxonomicTree tree, Taxon taxon);
 371
 372         public int countAllRelationships();
 373
 374         public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
 375         public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath);
 376         public String getPhylumName(TaxonNameBase name);
 377
 378         public long deleteSynonymRelationships(Synonym syn);
 379         /**
 380          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 381          * depending on direction, where the supplied taxon is relatedTo or the supplied synonym is relatedFrom.
 382          *
 383          * @param taxonBase The taxon or synonym that is relatedTo or relatedFrom
 384          * @param type The type of SynonymRelationship (can be null)
 385          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 386          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 387          * @param orderHints Properties to order by
 388          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 389          * @param direction The direction of the relationship
 390          * @return a List of SynonymRelationship instances
 391          */
 392         public List<SynonymRelationship> listSynonymRelationships(
 393                         TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
 394                         List<OrderHint> orderHints, List<String> propertyPaths, Direction direction);
 395
 396         /**
 397          * @param tnb
 398          * @return
 399          */
 400         public Taxon findBestMatchingTaxon(String taxonName);
 401 }