cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/persistence/dao/taxon/ITaxonDao.java

   1 /**
   2 * Copyright (C) 2007 EDIT
   3 * European Distributed Institute of Taxonomy
   4 * http://www.e-taxonomy.eu
   5 *
   6 * The contents of this file are subject to the Mozilla Public License Version 1.1
   7 * See LICENSE.TXT at the top of this package for the full license terms.
   8 */
   9
  10 package eu.etaxonomy.cdm.persistence.dao.taxon;
  11
  12 import java.util.List;
  13 import java.util.Set;
  14 import java.util.UUID;
  15
  16 import org.hibernate.criterion.Criterion;
  17
  18 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  19 import eu.etaxonomy.cdm.model.common.UuidAndTitleCache;
  20 import eu.etaxonomy.cdm.model.common.RelationshipBase.Direction;
  21 import eu.etaxonomy.cdm.model.location.NamedArea;
  22 import eu.etaxonomy.cdm.model.name.NonViralName;
  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.dao.common.IIdentifiableDao;
  37 import eu.etaxonomy.cdm.persistence.dao.common.ITitledDao;
  38 import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
  39 import eu.etaxonomy.cdm.persistence.query.MatchMode;
  40 import eu.etaxonomy.cdm.persistence.query.OrderHint;
  41
  42 /**
  43  * @author a.mueller
  44  *
  45  */
  46 public interface ITaxonDao extends IIdentifiableDao<TaxonBase>, ITitledDao<TaxonBase> {
  47
  48         /**
  49          * Returns a list of TaxonBase instances where the taxon.titleCache property matches the name parameter,
  50          * and taxon.sec matches the sec parameter.
  51          * @param name
  52          * @param sec
  53          * @return
  54          */
  55         public List<TaxonBase> getTaxaByName(String name, ReferenceBase sec);
  56
  57         /**
  58          * Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
  59          * where the taxonBase.name.nameCache property matches the String queryString, and taxon.sec matches the sec parameter.
  60          * @param name
  61          * @param sec
  62          * @return
  63          */
  64         public List<TaxonBase> getTaxaByName(String queryString, Boolean accepted, ReferenceBase sec);
  65
  66         /**
  67          * Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
  68          * where the taxonBase.name.nameCache property matches the String queryString.
  69          * @param queryString
  70          * @param matchMode
  71          * @param accepted
  72          * @param pageSize
  73          * @param pageNumber
  74          * @return
  75          */
  76         public List<TaxonBase> getTaxaByName(String queryString, MatchMode matchMode,
  77                         Boolean accepted, Integer pageSize, Integer pageNumber);
  78
  79
  80         /**
  81          * Returns a list of TaxonBase instances (or Taxon instances, if accepted == true, or Synonym instance, if accepted == false)
  82          * where the taxonBase.name.nameCache property matches the String queryString.
  83          * @param clazz
  84          * @param queryString
  85          * @param taxonomicTree TODO
  86          * @param matchMode
  87          * @param namedAreas TODO
  88          * @param pageSize
  89          * @param pageNumber
  90          * @param propertyPaths TODO
  91          * @return list of found taxa
  92          */
  93         public List<TaxonBase> getTaxaByName(Class<? extends TaxonBase> clazz, String queryString, TaxonomicTree taxonomicTree,
  94                         MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize, Integer pageNumber, List<String> propertyPaths);
  95
  96         /**
  97          * @param clazz
  98          * @param queryString
  99          * @param taxonomicTree TODO
 100          * @param matchMode
 101          * @param namedAreas
 102          * @param pageSize
 103          * @param pageNumber
 104          * @param propertyPaths
 105          * @return
 106          */
 107         public long countTaxaByName(Class<? extends TaxonBase> clazz, String queryString, TaxonomicTree taxonomicTree,
 108
 109                         MatchMode matchMode, Set<NamedArea> namedAreas);
 110
 111 //      /**
 112 //       * @param queryString
 113 //       * @param matchMode
 114 //       * @param accepted
 115 //       * @return
 116 //       */
 117 //      public Integer countTaxaByName(String queryString, MatchMode matchMode,
 118 //                      Boolean accepted);
 119
 120 //      /**
 121 //       * Returns a count of TaxonBase instances where the
 122 //       * taxon.name properties match the parameters passed.
 123 //       *
 124 //       * @param queryString search string
 125 //       * @param matchMode way how search string shall be matched: exact, beginning, or anywhere
 126 //       * @param selectModel all taxon base, taxa, or synonyms
 127 //       */
 128 //      public Integer countTaxaByName(String queryString, MatchMode matchMode, SelectMode selectMode);
 129
 130         /**
 131          * Computes all Taxon instances that do not have a taxonomic parent and has at least one child.
 132          * @return The List<Taxon> of root taxa.
 133          * @deprecated obsolete when using taxonomicTree
 134          */
 135         public List<Taxon> getRootTaxa(ReferenceBase sec);
 136
 137
 138         /**
 139          * Computes all Taxon instances that do not have a taxonomic parent.
 140          * @param sec The concept reference that the taxon belongs to
 141          * @param cdmFetch not used yet !! TODO
 142          * @param onlyWithChildren if true only taxa are returned that have taxonomic children. <Br>Default: true.
 143          * @param withMisaplications if false only taxa are returned that have no isMisappliedNameFor relationship.
 144          * <Br>Default: true.
 145          * @return The List<Taxon> of root taxa.
 146          * @deprecated obsolete when using taxonomicTree
 147          */
 148         public List<Taxon> getRootTaxa(ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications);
 149
 150
 151         /**
 152          * Computes all Taxon instances which name is of a certain Rank.
 153          *
 154          * @param rank
 155          *            The rank of the taxon name
 156          * @param sec
 157          *            The concept reference that the taxon belongs to
 158          * @param cdmFetch
 159          *            not used yet !! TODO
 160          * @param onlyWithChildren
 161          *            if true only taxa are returned that have taxonomic children. <Br>
 162          *            Default: true.
 163          * @param withMisaplications
 164          *            if false only taxa are returned that have no
 165          *            isMisappliedNameFor relationship.
 166          * @param propertyPaths
 167          *            properties to be initialized, For detailed description and
 168          *            examples <b>please refer to:</b>
 169          *            {@link BeanInitializer#initialize(Object, List)}. <Br>
 170          *            Default: true.
 171          * @return The List<Taxon> of root taxa.
 172          * @deprecated obsolete when using taxonomicTree
 173          */
 174         public List<Taxon>
 175         getRootTaxa(Rank rank, ReferenceBase sec, CdmFetch cdmFetch, Boolean onlyWithChildren, Boolean withMisapplications, List<String> propertyPaths);
 176
 177                 /**
 178          * TODO necessary?
 179          * @param pagesize max maximum number of returned taxa
 180          * @param page page to start, with 0 being first page
 181          * @return
 182          */
 183         public List<TaxonBase> getAllTaxonBases(Integer pagesize, Integer page);
 184
 185
 186         /**
 187          * @param limit
 188          * @param start
 189          * @return
 190          */
 191         public List<Taxon> getAllTaxa(Integer limit, Integer start);
 192
 193         /**
 194          * @param limit
 195          * @param start
 196          * @return
 197          */
 198         public List<Synonym> getAllSynonyms(Integer limit, Integer start);
 199
 200         public List<RelationshipBase> getAllRelationships(Integer limit, Integer start);
 201
 202         public int countAllRelationships();
 203
 204         /**
 205          * Find taxa by searching for @{link NameBase}
 206          * @param queryString
 207          * @param matchMode
 208          * @param page
 209          * @param pagesize
 210          * @param onlyAcccepted
 211          * @return
 212          */
 213         public List<Taxon> findByName(String queryString, MatchMode matchMode, int page, int pagesize, boolean onlyAcccepted);
 214
 215         /**
 216          * @param queryString
 217          * @param matchMode
 218          * @param onlyAcccepted
 219          * @return
 220          */
 221         public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted);
 222
 223         /**
 224          * @param queryString
 225          * @param matchMode
 226          * @param onlyAcccepted
 227          * @param criteria
 228          * @return
 229          */
 230         public int countMatchesByName(String queryString, MatchMode matchMode, boolean onlyAcccepted, List<Criterion> criteria);
 231
 232         /**
 233          * Returns a count of the TaxonRelationships (of where relationship.type ==
 234          * type, if this argument is supplied) where the supplied taxon either is
 235          * relatedFrom or relatedTo depending on the <code>direction</code>
 236          * parameter.
 237          *
 238          * @param taxon
 239          *            The taxon that is relatedFrom
 240          * @param type
 241          *            The type of TaxonRelationship (can be null)
 242          * @param direction
 243          *            specifies the direction of the relationship
 244          * @return the number of TaxonRelationship instances
 245          */
 246         public int countTaxonRelationships(Taxon taxon, TaxonRelationshipType type,
 247                         Direction direction);
 248
 249         /**
 250          * Returns the TaxonRelationships (of where relationship.type == type, if
 251          * this argument is supplied) where the supplied taxon either is
 252          * relatedFrom or relatedTo depending on the <code>direction</code>
 253          * parameter.
 254          *
 255          * @param taxon
 256          *            The taxon that is relatedTo
 257          * @param type
 258          *            The type of TaxonRelationship (can be null)
 259          * @param pageSize
 260          *            The maximum number of relationships returned (can be null for
 261          *            all relationships)
 262          * @param pageNumber
 263          *            The offset (in pageSize chunks) from the start of the result
 264          *            set (0 - based)
 265          * @param orderHints
 266          *            Properties to order by
 267          * @param propertyPaths
 268          *            Properties to initialize in the returned entities, following
 269          *            the syntax described in
 270          *            {@link BeanInitializer#initialize(Object, List)}
 271          * @param direction
 272          *            specifies the direction of the relationship
 273          * @return a List of TaxonRelationship instances
 274          */
 275         public List<TaxonRelationship> getTaxonRelationships(Taxon taxon,
 276                         TaxonRelationshipType type, Integer pageSize, Integer pageNumber,
 277                         List<OrderHint> orderHints, List<String> propertyPaths,
 278                         Direction direction);
 279
 280         /**
 281          * Returns a count of the SynonymRelationships (of where relationship.type == type,
 282          *  if this arguement is supplied) where the supplied taxon is relatedTo.
 283          *
 284          * @param taxon The taxon that is relatedTo
 285          * @param type The type of SynonymRelationship (can be null)
 286          * @return the number of SynonymRelationship instances
 287          */
 288         public int countSynonyms(Taxon taxon, SynonymRelationshipType type);
 289
 290         /**
 291          * Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied)
 292          * where the supplied taxon is relatedTo.
 293          *
 294          * @param taxon The taxon that is relatedTo
 295          * @param type The type of SynonymRelationship (can be null)
 296          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 297          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 298          * * @param orderHints Properties to order by
 299          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 300          * @return a List of SynonymRelationship instances
 301          */
 302         public List<SynonymRelationship> getSynonyms(Taxon taxon, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 303
 304         /**
 305          * Returns a count of the SynonymRelationships (of where relationship.type == type,
 306          *  if this arguement is supplied) where the supplied synonym is relatedFrom.
 307          *
 308          * @param taxon The synonym that is relatedFrom
 309          * @param type The type of SynonymRelationship (can be null)
 310          * @return the number of SynonymRelationship instances
 311          */
 312         public int countSynonyms(Synonym synonym, SynonymRelationshipType type);
 313
 314         /**
 315          * Returns the SynonymRelationships (of where relationship.type == type, if this arguement is supplied)
 316          * where the supplied synonym is relatedFrom.
 317          *
 318          * @param taxon The synonym that is relatedFrom
 319          * @param type The type of SynonymRelationship (can be null)
 320          * @param pageSize The maximum number of relationships returned (can be null for all relationships)
 321          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 322          * * @param orderHints Properties to order by
 323          * @param propertyPaths Properties to initialize in the returned entities, following the syntax described in {@link BeanInitializer#initialize(Object, List)}
 324          * @return a List of SynonymRelationship instances
 325          */
 326         public List<SynonymRelationship> getSynonyms(Synonym synoynm, SynonymRelationshipType type, Integer pageSize, Integer pageNumber, List<OrderHint> orderHints, List<String> propertyPaths);
 327
 328         /**
 329          * Returns a count of TaxonBase instances where the
 330          * taxon.name properties match the parameters passed.
 331          *
 332          * @param clazz
 333          * @param uninomial
 334          * @param infragenericEpithet
 335          * @param specificEpithet
 336          * @param infraspecificEpithet
 337          * @param rank
 338          * @return a count of TaxonBase instances
 339          */
 340         public int countTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet,String specificEpithet, String infraspecificEpithet, Rank rank);
 341
 342         /**
 343          * Returns a list of TaxonBase instances where the
 344          * taxon.name properties match the parameters passed. In order to search for any string value, pass '*', passing the string value of
 345          * <i>null</i> will search for those taxa with a value of null in that field
 346          *
 347          * @param clazz optionally filter by class (can be null to return all taxa)
 348          * @param uninomial
 349          * @param infragenericEpithet
 350          * @param specificEpithet
 351          * @param infraspecificEpithet
 352          * @param rank
 353          * @param pageSize The maximum number of taxa returned (can be null for all matching taxa)
 354          * @param pageNumber The offset (in pageSize chunks) from the start of the result set (0 - based)
 355          * @return a list of TaxonBase instances
 356          */
 357         public List<TaxonBase> findTaxaByName(Class<? extends TaxonBase> clazz, String uninomial, String infragenericEpithet, String specificEpithet, String infraspecificEpithet, Rank rank, Integer pageSize, Integer pageNumber);
 358
 359         /**
 360          *
 361          * @return
 362          */
 363         public List<UuidAndTitleCache<TaxonNode>> getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByTaxonomicTree(TaxonomicTree taxonomicTree);
 364
 365         public List<TaxonBase> getTaxaByCommonName(String queryString, TaxonomicTree taxonomicTree,
 366                         MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageSize,
 367                         Integer pageNumber, List<String> propertyPaths);
 368         /**
 369          * creates all inferred synonyms for the species in the tree and insert it to the database
 370          * @param tree
 371          * @return List of inferred synonyms
 372          */
 373         //public List<Synonym> insertAllInferredSynonymy(TaxonomicTree tree);
 374         /**
 375          * creates all inferred synonyms for the taxon in the taxonomic tree, but do not insert it to the database
 376          * @param taxon
 377          * @param tree
 378          * @return list of inferred synonyms
 379          */
 380         public List<Synonym>  createAllInferredSynonyms(Taxon taxon, TaxonomicTree tree);
 381         /**
 382          * creates the specified inferred synonyms for the taxon in the taxonomic tree, but do not insert it to the database
 383          * @param taxon
 384          * @param tree
 385          * @return list of inferred synonyms
 386          */
 387         public List<Synonym> createInferredSynonyms(Taxon taxon, TaxonomicTree tree, SynonymRelationshipType type);
 388
 389         public List<TaxonNameBase> findIdenticalTaxonNames(List<String> propertyPath);
 390         public String getPhylumName(TaxonNameBase name);
 391
 392         public long countTaxaByCommonName(String searchString,
 393                         TaxonomicTree taxonomicTree, MatchMode matchMode,
 394                         Set<NamedArea> namedAreas);
 395
 396         public long deleteSynonymRelationships(Synonym syn);
 397
 398         public List<UUID> findIdenticalTaxonNameIds(List<String> propertyPath);
 399
 400         public List<TaxonNameBase> findIdenticalNamesNew(List <String> propertyPaths);
 401
 402
 403         public Integer countSynonymRelationships(TaxonBase taxonBase,
 404                         SynonymRelationshipType type, Direction relatedfrom);
 405
 406         public List<SynonymRelationship> getSynonymRelationships(TaxonBase taxonBase,
 407                         SynonymRelationshipType type, Integer pageSize, Integer pageNumber,
 408                         List<OrderHint> orderHints, List<String> propertyPaths,
 409                         Direction relatedfrom);
 410
 411
 412 }