cdmlib-model/src/main/java/eu/etaxonomy/cdm/model/common/TermType.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.model.common;
  12
  13 import java.io.Serializable;
  14 import java.util.Set;
  15 import java.util.UUID;
  16
  17 import javax.lang.model.element.Modifier;
  18 import javax.xml.bind.annotation.XmlEnum;
  19 import javax.xml.bind.annotation.XmlEnumValue;
  20
  21 import org.apache.log4j.Logger;
  22
  23 import eu.etaxonomy.cdm.model.agent.Institution;
  24 import eu.etaxonomy.cdm.model.description.CategoricalData;
  25 import eu.etaxonomy.cdm.model.description.DescriptionBase;
  26 import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
  27 import eu.etaxonomy.cdm.model.description.Distribution;
  28 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  29 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  30 import eu.etaxonomy.cdm.model.description.StateData;
  31 import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
  32 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  33 import eu.etaxonomy.cdm.model.description.TextData;
  34 import eu.etaxonomy.cdm.model.location.NamedArea;
  35 import eu.etaxonomy.cdm.model.location.Point;
  36 import eu.etaxonomy.cdm.model.media.Rights;
  37 import eu.etaxonomy.cdm.model.molecular.Amplification;
  38 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  39 import eu.etaxonomy.cdm.model.name.NameRelationship;
  40 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  41 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  42 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  43 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  44 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  45 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  46 import eu.etaxonomy.cdm.model.taxon.Synonym;
  47 import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
  48 import eu.etaxonomy.cdm.model.taxon.Taxon;
  49 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  50 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  51
  52
  53
  54 /**
  55  * The term type is used to define the type of a {@link TermBase term}, may it be a vocabulary or a defined term.<BR>
  56  * It is used to define in which context a term may be used. From v3.3 on this replaces the semantic part of the subclasses
  57  * of the class {@link DefinedTermBase}. E.g. before v3.3 a term defining a sex and a term defining a stage had to different
  58  * classes Sex and Stage. With v3.3 they both became {@link DefinedTerm}s but with different types.<BR>
  59  * The type of a term and the type of its vocabulary should be the same. Before v3.3 it was not always possible to define
  60  * what the context of an (empty) vocabulary is.
  61  * In future versions this enum may also be expressed as a term, not an enum. For now the general policy is to
  62  * transform former classes to general classes with enums as their types.
  63  *
  64  * @author a.mueller
  65  * @created 11.06.2013
  66  */
  67 @XmlEnum
  68 public enum TermType implements IEnumTerm<TermType>, Serializable{
  69
  70         //0
  71         /**
  72          * Unknown term type is the type to be used if no information is available about the type.
  73          * In the current model this type should never be used. However, it is a placeholder in case
  74          * we find an appropriate usage in future.
  75          */
  76         @XmlEnumValue("Unknown")
  77         Unknown(UUID.fromString("b2836c89-3b1d-4758-ba6d-568ef8d6fbc4"), "Unknown term type","UNK", null),
  78
  79         //1
  80         /**
  81          * Term type to represent languages.
  82          */
  83         @XmlEnumValue("Language")
  84         Language(UUID.fromString("5591dc6c-ad1f-4abd-b6c2-4852ea8e46df"), "Language", "LA", null),
  85
  86         //2
  87         /**
  88          * Term type for areas.
  89          */
  90         @XmlEnumValue("NamedArea")
  91         NamedArea(UUID.fromString("8c9a0bc9-da91-478d-bc8b-44b11565e160"), "Named area", "NA", null),
  92
  93         //3
  94         /**
  95          * Term type for taxonomic ranks.
  96          */
  97         @XmlEnumValue("Rank")
  98         Rank(UUID.fromString("8d26b6a9-8a89-45d5-8358-49c3e4f30ade"), "Rank", "RK", null),
  99
 100         //4
 101         /**
 102          * Term type for descriptive features.
 103          * @see DescriptionElementBase
 104          */
 105         @XmlEnumValue("Feature")
 106         Feature(UUID.fromString("b866a1d6-f962-4c23-bb8e-a3b66d33aedc"), "Feature", "FE", null),
 107
 108         //5
 109         /**
 110          * Term type for annotation types.
 111          * @see Annotation
 112          */
 113         @XmlEnumValue("AnnotationType")
 114         AnnotationType(UUID.fromString("c3aabb64-6174-4152-95b1-7cec57e485cf"), "Annotation type", "ANT", null),
 115
 116         //6
 117         /**
 118          * Term type for marker types.
 119          * @see Marker
 120          */
 121         @XmlEnumValue("MarkerType")
 122         MarkerType(UUID.fromString("d28a1bf8-95ed-483a-8f02-3515b14998e0"), "MarkerType", "MKT", null),
 123
 124         //7
 125         /**
 126          * Term type for extension types.
 127          * @see Extension
 128          */
 129         @XmlEnumValue("ExtensionType")
 130         ExtensionType(UUID.fromString("12f5c03b-528a-4909-b81b-e525feabc97c"), "Extension type", "EXT", null),
 131
 132         //8
 133         /**
 134          * Term type for derivation event types.
 135          * @see DerivationEvent
 136          */
 137         @XmlEnumValue("DerivationEventType")
 138         DerivationEventType(UUID.fromString("ba8e4b10-c792-42e7-a3f5-874708f10094"), "Derivation event type", "DET", null),
 139
 140         //9
 141         /**
 142          * Term type for presence or absence status
 143          * @see Distribution
 144          */
 145         @XmlEnumValue("PresenceAbsenceTerm")
 146         PresenceAbsenceTerm(UUID.fromString("f6b80f88-c8c5-456b-bbd6-d63ecf35606e"), "Presence or absence term", "PAT", null),
 147
 148         //10
 149         /**
 150          * Term type for the taxonomic nomenclatural status of a {@link TaxonNameBase taxon name}.
 151          * @see NomenclaturalStatus
 152          */
 153         @XmlEnumValue("NomenclaturalStatusType")
 154         NomenclaturalStatusType(UUID.fromString("c1acb71a-1d11-4305-8818-c2268d341742"), "Nomenclatural status type", "NST", null),
 155
 156         //11
 157         /**
 158          * Term type for the type of a name relationship between {@link TaxonNameBase taxon names}
 159          * @see NameRelationship
 160          */
 161         @XmlEnumValue("NameRelationshipType")
 162         NameRelationshipType(UUID.fromString("acd8189a-23b9-4a53-8f48-1d2aa270a6ba"), "Name relationship type", "NRT"),
 163
 164         //12
 165         /**
 166          * Term type for the type of a hybrid relationship between {@link TaxonNameBase taxon names}
 167          * @see HybridRelationship
 168          */
 169         @XmlEnumValue("HybridRelationshipType")
 170         HybridRelationshipType(UUID.fromString("aade9e61-eaa1-40fe-9eb1-40f9e8ae1114"), "Hybrid relationship type", "HRT"),
 171
 172         //13
 173         /**
 174          * Term type for the type of a synonym relationship between 2 {@link TaxonBase taxa}
 175          * @see SynonymRelationship
 176          * @see Synonym
 177          * @see TaxonBase
 178          */
 179         @XmlEnumValue("SynonymRelationshipType")
 180         SynonymRelationshipType(UUID.fromString("1eb4fee0-7716-4531-a9ed-a95327f1f4bb"), "Synonym relationship type", "SRT"),
 181
 182         //14
 183         /**
 184          * Term type for the type of a taxonomic concept relationship between
 185          * 2 {@link Taxon accepted taxa}  with different secundum referece.
 186          * @see TaxonRelationship
 187          * @see Taxon
 188          */
 189         @XmlEnumValue("TaxonRelationshipType")
 190         TaxonRelationshipType(UUID.fromString("2d4b281c-142e-42c5-8eb5-1747592b54d8"), "Taxon relationship type", "TRT"),
 191
 192         //15
 193         /**
 194          * Term type for the type of a typification of a taxonomic name
 195          * with a rank higher then species.
 196          * @see eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus
 197          * @see NameTypeDesignation
 198          */
 199         @XmlEnumValue("NameTypeDesignationStatus")
 200         NameTypeDesignationStatus(UUID.fromString("d3860be6-8a08-4fff-984a-6ee8b42937c9"), "Name type designation status", "NTD"),
 201
 202         //16
 203         /**
 204          * Term type for the type of a typification of a taxonomic name
 205          * with a rank equal or lower then species.
 206          * @see {@link eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus}
 207          * @see SpecimenTypeDesignation
 208          */
 209         @XmlEnumValue("SpecimenTypeDesignationStatus")
 210         SpecimenTypeDesignationStatus(UUID.fromString("4014d7d4-f2dd-4328-8015-357a1a77c1ed"), "Specimen type designation status", "STD"),
 211
 212         //17
 213         /**
 214          * Term type for an institution type.
 215          * @see Institution
 216          */
 217         @XmlEnumValue("InstitutionType")
 218         InstitutionType(UUID.fromString("09d78265-18b5-4352-b154-d2f39e84d3f3"), "Institution type", "IT", null),
 219
 220         //18
 221         /**
 222          * Term type for a named area type.
 223          * @see NamedArea
 224          * @see eu.etaxonomy.cdm.model.location.NamedAreaType
 225          */
 226         @XmlEnumValue("NamedAreaType")
 227         NamedAreaType(UUID.fromString("6a9aba35-6272-4373-8386-000cf95b729e"), "Named area type", "NAT", null),
 228
 229         //19
 230         /**
 231          * Term type for a named area level.
 232          * @see NamedArea
 233          * @see eu.etaxonomy.cdm.model.location.NamedAreaLevel
 234          */
 235         @XmlEnumValue("NamedAreaLevel")
 236         NamedAreaLevel(UUID.fromString("62c16c74-dc79-4970-9031-bb1504be46f5"), "Named area level", "NAL", null),
 237
 238         //20
 239         /**
 240          * Term type for rights.
 241          * @see Rights
 242          */
 243         @XmlEnumValue("RightsType")
 244         RightsType(UUID.fromString("80e06b04-8d0d-4bd5-bcd6-d35f73c24d55"), "Rights type", "RT", null),
 245
 246         //21
 247         /**
 248          * Term type for a measurement unit.
 249          * @see MeasurementUnit
 250          */
 251         @XmlEnumValue("MeasurementUnit")
 252         MeasurementUnit(UUID.fromString("f9e6c44f-f0d6-428b-9bc0-bb00a6514883"), "Measurement unit", "MU", null),
 253
 254         //22
 255         /**
 256          * Term type for a statistical measure.
 257          * @see eu.etaxonomy.cdm.model.description.StatisticalMeasure
 258          * @see StatisticalMeasurementValue
 259          */
 260         @XmlEnumValue("StatisticalMeasure")
 261         StatisticalMeasure(UUID.fromString("a22d19cd-a342-4af2-b156-d688a7aa8a6b"), "Statistical measure", "SM", null),
 262
 263         //23
 264         @XmlEnumValue("MaterialOrMethod")
 265         MaterialOrMethod(UUID.fromString("285a1406-a606-46b9-b0a4-717748296e50"), "Material or Method", "MOM"),
 266
 267         //23a
 268         @XmlEnumValue("Material")
 269         Material(UUID.fromString("58499bc1-9808-4e03-861c-4325ca889515"), "Material", "MAT", MaterialOrMethod),
 270
 271         //23b
 272         @XmlEnumValue("Method")
 273         Method(UUID.fromString("527fc141-7fdf-43c1-9d46-20be13c2590c"), "Method", "MET", MaterialOrMethod),
 274
 275
 276 //      //23c TODO required??
 277 //      @XmlEnumValue("PreservationMethod")   --> Method
 278 //      PreservationMethod(UUID.fromString("9cadbee4-22b5-40f5-bb37-e4f5340d246e"), "Preservation method", "PRM", MaterialOrMethod),
 279 //
 280 //      //23d TODO required??  --> Material
 281 //      @XmlEnumValue("PreservationMedium")
 282 //      PreservationMedium(UUID.fromString("c6269a06-6954-4838-a7a7-7f94ba372f3d"), "Preservation medium", "PME", MaterialOrMethod),
 283
 284
 285         //24
 286         /**
 287          * This type represents possible modulations for the validity of
 288          * information pieces ({@link DescriptionElementBase} description elements).
 289          * It can cover probability ("perhaps"), frequency ("often") intensity ("very"),
 290          * timing ("spring") and other domains. Its instances can be grouped to build
 291          * different controlled {@link TermVocabulary term vocabularies}.
 292          * <P>
 293          * This class corresponds to GeneralModifierNLDType according to
 294          * the SDD schema.
 295          * This class is a generalization of {@link #Scope} and {@link #DeterminationModifier}
 296          *
 297          * @see DescriptionElementBase#getModifiers()
 298          * @see StateData#getModifiers()
 299          */
 300         @XmlEnumValue("Modifier")
 301         Modifier(UUID.fromString("97c4db67-ccf5-40bf-9fb8-83fb7446a364"), "Modifier", "MO", null),
 302
 303         //25
 304         /**
 305          * The type representing restrictions for the validity of
 306          * {@link TaxonDescription taxon descriptions} and others.
 307          * This could include not only Stage (life stage) and Sex
 308          * but also for instance particular organism parts or seasons.<BR>
 309          * Scope is a specialization of {@link #Modifier} and a generalization of
 310          * {@link #Sex} and {@link #Stage}
 311          *
 312          * @see Modifier
 313          * @see DescriptionElementBase
 314          * @see TaxonDescription
 315          * @see TaxonDescription#getScopes()
 316          */
 317         @XmlEnumValue("Scope")
 318         Scope(UUID.fromString("8862b66e-9059-4ea4-885e-47a373357075"), "Scope", "SCO", Modifier),
 319
 320         //26
 321         /** The stage type represents the restriction (scope) concerning the life stage for
 322          * the applicability of {@link TaxonDescription taxon descriptions}. The life stage of a
 323          * {@link SpecimenOrObservationBase specimen or observation}
 324          * does not belong to a {@link SpecimenDescription specimen description} but is an attribute of
 325          * the specimen itself.<BR>
 326          *
 327          * Stage is a specialization of {@link #Scope}.
 328          */
 329         @XmlEnumValue("Stage")
 330         Stage(UUID.fromString("cf411ef0-8eee-4461-99e9-c03f4f0a1656"), "Stage", "STG", Scope),
 331
 332         //26a
 333         /** The kind-of-unit type represents the restriction (scope) concerning the part(s) of an
 334          * organism or the class of materials represented by a specimen or observation or described
 335          * by a {@link DescriptionBase taxon or specimen description}.<BR>
 336          * In a {@link DescriptionBase description} it can be used as a {@link #Modifier} or
 337      * a {@link #Scope} and therefore it is a specialization of {@link #Scope}.<BR>
 338          * The kind-of-unit of a {@link SpecimenOrObservationBase specimen or observation}
 339          * should be added as an {@link SpecimenOrObservationBase#getKindOfUnit() kindOfUnit} attribute
 340          * if the specimen is only a part of an organism and this part is described by the part-of-unit.
 341          * If only a part of a specimen is described in a {@link SpecimenDescription specimen description}
 342          * the kind-of-unit should be used as a {@link DescriptionBase description} scope
 343          * (not yet implemented for specimen descriptions) or as a modifier in a
 344          * {@link DescriptionElementBase description item}.<BR><BR>
 345          *
 346          * Value examples are: fruits, seeds, tissue, gDNA, leaves, ... <BR>
 347      *
 348          * KindOfUnit is a Specialization of {@link #Scope}.
 349          *
 350          * @see SpecimenOrObservationBase#getKindOfUnit()
 351          * @see TaxonDescription#getScopes()
 352          * @see DescriptionElementBase#getModifiers()
 353          * @see StateData#getModifiers()
 354          */
 355         @XmlEnumValue("KindOfUnit")
 356         KindOfUnit(UUID.fromString("e3edf086-ff7b-4e58-ab1c-d509352fe5f4"), "Kind of Unit", "KOU", Scope),
 357
 358
 359         //27
 360         /**
 361          * The type represents the restriction concerning the sex for
 362          * the applicability of {@link TaxonDescription taxon descriptions} or others. The sex of a
 363          * {@link SpecimenOrObservationBase specimen or observation}
 364          * does not belong to a {@link SpecimenDescription specimen description} but is an attribute of
 365          * the specimen itself.<BR>
 366          *
 367          * Sex is a specialization of {@link #Scope}.
 368          */
 369         @XmlEnumValue("Sex")
 370         Sex(UUID.fromString("4046f91f-063b-4b84-b34a-6245c2abc06f"), "Sex", "SEX", Scope),
 371
 372         //28
 373         /**
 374          * Term type for a reference system of a geographic information.
 375          * @see Point
 376          * @see Point#getReferenceSystem()
 377          */
 378         @XmlEnumValue("ReferenceSystem")
 379         ReferenceSystem(UUID.fromString("b8cfa986-ef90-465e-9609-1dadae2a0f5b"), "Reference system", "RS", null),
 380
 381         //29
 382         /**
 383          * Term type for a term representing a state for {@link CategoricalData categorical data}
 384          * @see CategoricalData#getStateData()
 385          * @see StateData#getState()
 386          */
 387         @XmlEnumValue("State")
 388         State(UUID.fromString("5e5b8b60-7300-440a-8706-72fbf31a594f"), "State", "STA", null),
 389
 390         //30
 391         /**
 392          * Term type representing a natural language term.
 393          */
 394         @XmlEnumValue("NaturalLanguageTerm")
 395         NaturalLanguageTerm(UUID.fromString("9a42ac4e-c175-4633-8b31-74ba8203566a"), "Natural language term", "NLT", null),
 396
 397
 398         //31
 399         /**
 400          * Term type for a text format.
 401          * @see TextData
 402          */
 403         @XmlEnumValue("TextFormat")
 404         TextFormat(UUID.fromString("d26cfdb4-baeb-43d0-a51b-a3428d838790"), "Text format", "TF", null),
 405
 406         //32
 407         /**
 408          * TODO
 409          *
 410          * Determination modifier is a specialization of {@link #Modifier}.
 411          */
 412         @XmlEnumValue("DeterminationModifier")
 413         DeterminationModifier(UUID.fromString("ce910516-bc5d-4ac5-be4d-f3c14c27dd85"), "Determination modifier", "DMO", Modifier),
 414
 415         //33
 416         /**
 417          * A marker is a region on a DNA which is adressed in an {@link Amplification amplification process}.
 418          * It is very similar to a locus, a term which is often used as a synonym. However, a locus is correctly
 419          * defining one concrete place on a given DNA and therefore is more specific. As this specific information
 420          * is usually not available the marker information is provided instead.
 421          * @see Amplification
 422          * @see Amplification#getMarker()
 423          * @see Sequencing
 424          * @see Sequencing#getMarker()
 425          */
 426         @XmlEnumValue("DnaMarker")
 427         DnaMarker(UUID.fromString("7fdddb4f-b0ec-4ce0-bc28-dc94e30e8252"), "DNA Marker", "DMA", null),
 428         ;
 429
 430         @SuppressWarnings("unused")
 431         private static final Logger logger = Logger.getLogger(TermType.class);
 432
 433         private TermType(UUID uuid, String defaultString, String key){
 434                 this(uuid, defaultString, key, null);
 435         }
 436
 437         private TermType(UUID uuid, String defaultString, String key, TermType parent){
 438                 delegateVocTerm = EnumeratedTermVoc.addTerm(getClass(), this, uuid, defaultString, key, parent);
 439         }
 440
 441
 442 // *************************** DELEGATE **************************************/
 443
 444         private static EnumeratedTermVoc<TermType> delegateVoc;
 445         private IEnumTerm<TermType> delegateVocTerm;
 446
 447         static {
 448                 delegateVoc = EnumeratedTermVoc.getVoc(TermType.class);
 449         }
 450
 451         @Override
 452         public String getKey(){return delegateVocTerm.getKey();}
 453
 454         @Override
 455     public String getMessage(){return delegateVocTerm.getMessage();}
 456
 457         @Override
 458     public String getMessage(Language language){return delegateVocTerm.getMessage(language);}
 459
 460         @Override
 461     public UUID getUuid() {return delegateVocTerm.getUuid();}
 462
 463         @Override
 464     public TermType getKindOf() {return delegateVocTerm.getKindOf();}
 465
 466         @Override
 467     public Set<TermType> getGeneralizationOf() {return delegateVocTerm.getGeneralizationOf();}
 468
 469         @Override
 470         public boolean isKindOf(TermType ancestor) {return delegateVocTerm.isKindOf(ancestor);  }
 471
 472         @Override
 473     public Set<TermType> getGeneralizationOf(boolean recursive) {return delegateVocTerm.getGeneralizationOf(recursive);}
 474
 475         public static TermType getByKey(String key){return delegateVoc.getByKey(key);}
 476     public static TermType getByUuid(UUID uuid) {return delegateVoc.getByUuid(uuid);}
 477
 478         /**
 479          * Returns a defined term base object corresoponding to this term type object
 480          *
 481          * @return a defined term base object
 482          */
 483     public DefinedTermBase getEmptyDefinedTermBase() {
 484         switch(this) {
 485                 case DeterminationModifier:
 486                 case Modifier:
 487                 case Scope:
 488                 case Sex:
 489                 case Stage:
 490                 case DnaMarker:
 491                         return DefinedTerm.NewInstance(this, null, "Untitled", null);
 492                 case Feature:
 493                         return eu.etaxonomy.cdm.model.description.Feature.NewInstance(null, "Untitled", null);
 494                 case State:
 495                         return eu.etaxonomy.cdm.model.description.State.NewInstance(null, "Untitled", null);
 496                 case MarkerType:
 497                         return eu.etaxonomy.cdm.model.common.MarkerType.NewInstance(null, "Untitled", null);
 498                 case ExtensionType:
 499                         return eu.etaxonomy.cdm.model.common.ExtensionType.NewInstance(null, "Untitled", null);
 500                 case NamedArea:
 501                         return eu.etaxonomy.cdm.model.location.NamedArea.NewInstance(null, "Untitled", null);
 502                 case NamedAreaLevel:
 503                         return eu.etaxonomy.cdm.model.location.NamedAreaLevel.NewInstance(null, "Untitled", null);
 504                 case NamedAreaType:
 505                         return eu.etaxonomy.cdm.model.location.NamedAreaType.NewInstance(null, "Untitled", null);
 506                 default:
 507                         return null;
 508         }
 509     }
 510
 511
 512 }