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.Rank;
  24 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  25 import eu.etaxonomy.cdm.model.reference.ReferenceBase;
  26 import eu.etaxonomy.cdm.model.taxon.Synonym;
  27 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  28 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
  29 import eu.etaxonomy.cdm.model.taxon.Taxon;
  30 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  31 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
  32 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  33 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  34 import eu.etaxonomy.cdm.model.taxon.TaxonomicTree;
  35 import eu.etaxonomy.cdm.persistence.dao.BeanInitializer;
  36 import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
  37 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  38
  39
  40 public interface ITaxonService extends IIdentifiableEntityService<TaxonBase>{
  41
  42         /**
  43          * Computes all taxon bases.
  44          * FIXME could substitute with list(Synonym.class, limit, start)
  45          * @param limit
  46          * @param start
  47          * @return
  48          */
  49         public List<Synonym> getAllSynonyms(int limit, int start);
  50
  51         /**
  52          * Computes all taxon bases.
  53          * FIXME could substitute with list(Taxon.class, limit,start)
  54          * @param limit
  55          * @param start
  56          * @return
  57          */
  58         public List<Taxon> getAllTaxa(int limit, int start);
  59
  60         /**
  61          * Computes all Taxon instances that do not have a taxonomic parent and has at least one child.
  62          * @param sec The concept reference that the taxon belongs to
  63          * @return The List<Taxon> of root taxa.
  64          * @deprecated obsolete when using taxonomicTree
  65          */
  66         public List<Taxon> getRootTaxa(ReferenceBase sec);
  67
  68
  69         /**
  70          * Computes all Taxon instances that do not have a taxonomic parent.
  71          * @param sec The concept reference that the taxon belongs to
  72          *
  73          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  74          * @return The List<Taxon> of root taxa.
  75          * @deprecated obsolete when using taxonomicTree
  76          */
  77         public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, boolean onlyWithChildren);
  78
  79         /**
  80          * Computes all Taxon instances that do not have a taxonomic parent.
  81          * @param sec The concept reference that the taxon belongs to
  82          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  83          * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  84          * the misapplied name are not returned.<Br>Default: true.
  85          * @return The List<Taxon> of root taxa.
  86          * @deprecated obsolete when using taxonomicTree
  87          */
  88         public List<Taxon> getRootTaxa(ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications);
  89
  90         /**
  91          * Computes all Taxon instances which name is of a certain Rank.
  92          * @param rank The rank of the taxon name
  93          * @param sec The concept reference that the taxon belongs to
  94          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
  95          * @param withMisapplications if false taxa that have at least one misapplied name relationship in which they are
  96          * the misapplied name are not returned.<Br>Default: true.
  97          * @param propertyPaths
  98          *            properties to be initialized, For detailed description and
  99          *            examples <b>please refer to:</b>
 100          *            {@link BeanInitializer#initialize(Object, List)}. <Br>
 101          *            Default: true.
 102          * @return The List<Taxon> of root taxa.
 103          * @deprecated obsolete when using taxonomicTree
 104          */
 105         public List<Taxon> getRootTaxa(Rank rank, ReferenceBase sec, boolean onlyWithChildren, boolean withMisapplications, List<String> propertyPaths);
 106
 107         /**
 108          * Computes all relationships.
 109          * @param limit
 110          * @param start
 111          * @return
 112          */
 113     public List<RelationshipBase> getAllRelationships(int limit, int start);
 114
 115         /**
 116          * Returns TaxonRelationshipType vocabulary
 117          * @return
 118          * @deprecated use TermService#getVocabulary(VocabularyType) instead
 119          */
 120         public OrderedTermVocabulary<TaxonRelationshipType> getTaxonRelationshipTypeVocabulary();
 121
 122         /**
 123          * Returns a list of taxa that matches the name string and the sec reference
 124          * @param name the name string to search for
 125          * @param sec the taxons sec reference
 126          * @return a list of taxa matching the name and the sec reference
 127          */
 128         public List<TaxonBase> searchTaxaByName(String name, ReferenceBase sec);
 129
 130         /**
 131          * Changes an accepted taxon to a synonym of another taxon.
 132          *
 133          * @param oldTaxonNode
 134          *                              the <code>TaxonNode</code> of the accepted taxon that will be changed into a synonym
 135          * @param newAcceptedTaxonNode
 136          *                              the <code>TaxonNode</code> of the accepted taxon, the old taxon will become a synonym of
 137          * @param synonymType
 138          *                              <code>SynonymRelationshipType</code> to indicate whether hetero or homotypic
 139          * @param citation
 140          *                              the reference for this assumption
 141          * @param citationMicroReference
 142          *                              the micro citation
 143          * @return
 144          *                              the newly created synonym
 145          */
 146         public Synonym changeAcceptedTaxonToSynonym (TaxonNode oldTaxonNode, TaxonNode newAcceptedTaxonNode, SynonymRelationshipType synonymType, ReferenceBase citation, String citationMicroReference);
 147
 148         /**
 149          * Swaps given synonym and accepted taxon.
 150          * In particular:
 151          * <ul>
 152          *              <li>A new accepted taxon with the synonyms name is created</li>
 153          *              <li>The synonym is deleted from the old accepted taxons synonym list</li>
 154          *              <li>A new synonym with the name of the old accepted taxon is created</li>
 155          *              <li>The newly created synonym get related to the newly created accepted taxon</li>
 156          * </ul>
 157          *
 158          * @param synonym
 159          * @param acceptedTaxon
 160          * @param synonymRelationshipType the relationship type the newly created synonym will have. Defaults to SYNONYM_OF
 161          */
 162         public void swapSynonymAndAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 163
 164         /**
 165          * Change a synonym into an accepted taxon and removes
 166          * the synonym relationship to the given accepted taxon.
 167          *
 168          * @param synonym
 169          *                              the synonym to change into an accepted taxon
 170          * @param acceptedTaxon
 171          *                              an accepted taxon, the synonym had a relationship to
 172          * @return
 173          *                              the newly created accepted taxon
 174          */
 175         public Taxon changeSynonymToAcceptedTaxon(Synonym synonym, Taxon acceptedTaxon);
 176
 177         /**
 178          * Change a synonym into a related concept
 179          *
 180          * @param synonym
 181          *                              the synonym to change into the concept taxon
 182          * @param toTaxon
 183          *                              the taxon the newly created concept should be related to
 184          * @param taxonRelationshipType
 185          *                              the type of relationship
 186          * @param citation
 187          * @param microcitation
 188          * @return
 189          *                              the newly created concept
 190          */
 191         public Taxon changeSynonymToRelatedTaxon(Synonym synonym, Taxon toTaxon, TaxonRelationshipType taxonRelationshipType, ReferenceBase citation, String microcitation);
 192
 193         /**
 194          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 195          * where the supplied taxon is relatedTo.
 196          *
 197          * @param taxon The taxon that is relatedTo
 198          * @param type The type of TaxonRelationship (can be null)
 199          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 200          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 201          * @param orderHints Properties to order by
 202          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 203          * @return a List of TaxonRelationship instances
 204          */
 205         public List<TaxonRelationship> listToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 206
 207
 208
 209         /**
 210          * Returns the TaxonRelationships (of where relationship.type == type, if this arguement is supplied)
 211          * where the supplied taxon is relatedTo.
 212          *
 213          * @param taxon The taxon that is relatedTo
 214          * @param type The type of TaxonRelationship (can be null)
 215          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 216          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 217          * @param orderHints Properties to order by
 218          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 219          * @return a Pager of TaxonRelationship instances
 220          */
 221         public Pager<TaxonRelationship> pageToTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 222
 223         /**
 224          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 225          * where the supplied taxon is relatedFrom.
 226          *
 227          * @param taxon The taxon that is relatedFrom
 228          * @param type The type of TaxonRelationship (can be null)
 229          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 230          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 231          * @param orderHints Properties to order by
 232          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 233          * @return a List of TaxonRelationship instances
 234          */
 235         public List<TaxonRelationship> listFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 236
 237
 238         /**
 239          * Returns the TaxonRelationships (of where relationship.type == type, if this argument is supplied)
 240          * where the supplied taxon is relatedFrom.
 241          *
 242          * @param taxon The taxon that is relatedFrom
 243          * @param type The type of TaxonRelationship (can be null)
 244          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 245          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 246          * @param orderHints Properties to order by
 247          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 248          * @return a Pager of TaxonRelationship instances
 249          */
 250         public Pager<TaxonRelationship> pageFromTaxonRelationships(Taxon taxon, TaxonRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 251
 252         /**
 253          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 254          * where the supplied synonym is relatedFrom.
 255          *
 256          * @param taxon The synonym that is relatedFrom
 257          * @param type The type of SynonymRelationship (can be null)
 258          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 259          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 260          * * @param orderHints Properties to order by
 261          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 262          * @return a Pager of SynonymRelationship instances
 263          */
 264         public Pager<SynonymRelationship> getSynonyms(Synonym synonym, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 265
 266         /**
 267          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 268          * where the supplied taxon is relatedTo.
 269          *
 270          * @param taxon The taxon that is relatedTo
 271          * @param type The type of SynonymRelationship (can be null)
 272          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 273          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 274          * * @param orderHints Properties to order by
 275          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 276          * @return a Pager of SynonymRelationship instances
 277          */
 278         public Pager<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 279
 280         public List<Synonym> getHomotypicSynonymsByHomotypicGroup(Taxon taxon, List<String> propertyPaths);
 281
 282         public List<List<Synonym>> getHeterotypicSynonymyGroups(Taxon taxon, List<String> propertyPaths);
 283
 284         /**
 285          * Returns a Paged List of TaxonBase instances where the default field matches the String queryString (as interpreted by the Lucene QueryParser)
 286          *
 287          * @param clazz filter the results by class (or pass null to return all TaxonBase instances)
 288          * @param queryString
 289          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 290          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 291          * @param orderHints
 292          *            Supports path like <code>orderHints.propertyNames</code> which
 293          *            include *-to-one properties like createdBy.username or
 294          *            authorTeam.persistentTitleCache
 295          * @param propertyPaths properties to be initialized
 296          * @return a Pager Taxon instances
 297          * @see <a href="http://lucene.apache.org/java/2_4_0/queryparsersyntax.html">Apache Lucene - Query Parser Syntax</a>
 298          */
 299         public Pager<TaxonBase> search(Class<? extends TaxonBase> clazz, String queryString, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 300
 301         /**
 302          * Returns a list of TaxonBase instances where the
 303          * taxon.name properties match the parameters passed.
 304          *
 305          * @param clazz optionally filter by class
 306          * @param uninomial
 307          * @param infragenericEpithet
 308          * @param specificEpithet
 309          * @param infraspecificEpithet
 310          * @param rank
 311          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 312          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 313          * @return a Pager of TaxonBase instances
 314          */
 315         public Pager<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 316
 317         /**
 318          * Returns a list of TaxonBase instances where the
 319          * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 320          * <i>null</i> will search for those taxa with a value of null in that field
 321          *
 322          * @param clazz optionally filter by class
 323          * @param uninomial
 324          * @param infragenericEpithet
 325          * @param specificEpithet
 326          * @param infraspecificEpithet
 327          * @param rank
 328          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 329          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 330          * @return a List of TaxonBase instances
 331          */
 332         public List<TaxonBase> listTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 333
 334         /**
 335          * Returns a list of IdentifiableEntity instances (in particular, TaxonNameBase and TaxonBase instances)
 336          * that match the properties specified in the configurator.
 337          * @param configurator
 338          * @return
 339          */
 340         public Pager<IdentifiableEntity> findTaxaAndNames(ITaxonServiceConfigurator configurator);
 341
 342         /**
 343          *
 344          * @param taxon
 345          * @param size
 346          * @param height
 347          * @param widthOrDuration
 348          * @param mimeTypes
 349          * @return
 350          */
 351         public List<MediaRepresentation> getAllMedia(Taxon taxon, int size, int height, int widthOrDuration, String[] mimeTypes);
 352
 353         public List<TaxonBase> findTaxaByID(Set<Integer> listOfIDs);
 354         /**
 355          * returns a list of inferred synonyms concerning the taxon with synonymrelationshiptype type
 356          * @param tree
 357          * @param taxon
 358          * @param type
 359          * @return
 360          */
 361         public List<Synonym> createInferredSynonyms(TaxonomicTree tree, Taxon taxon, SynonymRelationshipType type);
 362         /**
 363          * returns a list of all inferred synonyms (inferred epithet, inferred genus and potential combination) concerning the taxon
 364          * @param tree
 365          * @param taxon
 366          * @return
 367          */
 368         public List<Synonym> createAllInferredSynonyms(TaxonomicTree tree, Taxon taxon);
 369
 370         public int countAllRelationships();
 371
 372         public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
 373         public List<TaxonNameBase> findIdenticalTaxonNameIds(List<String> propertyPath);
 374         public String getPhylumName(TaxonNameBase name);
 375
 376         public long deleteSynonymRelationships(Synonym syn);
 377         /**
 378          * Returns the SynonymRelationships (of where relationship.type == type, if this argument is supplied)
 379          * depending on direction, where the supplied taxon is relatedTo or the supplied synonym is relatedFrom.
 380          *
 381          * @param taxonBase The taxon or synonym that is relatedTo or relatedFrom
 382          * @param type The type of SynonymRelationship (can be null)
 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 Properties to order by
 386          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 387          * @param direction The direction of the relationship
 388          * @return a List of SynonymRelationship instances
 389          */
 390         public List<SynonymRelationship> listSynonymRelationships(
 391                         TaxonBase taxonBase, SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
 392                         List<OrderHint> orderHints, List<String> propertyPaths, Direction direction);
 393 }