cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/sdd/out/SDDDataSet.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.io.sdd.out;
  11
  12 import java.util.ArrayList;
  13 import java.util.Collection;
  14 import java.util.HashSet;
  15 import java.util.List;
  16 import java.util.Set;
  17
  18 import javax.xml.bind.annotation.XmlAccessType;
  19 import javax.xml.bind.annotation.XmlAccessorType;
  20 import javax.xml.bind.annotation.XmlElement;
  21 import javax.xml.bind.annotation.XmlElementWrapper;
  22 import javax.xml.bind.annotation.XmlElements;
  23 import javax.xml.bind.annotation.XmlRootElement;
  24 import javax.xml.bind.annotation.XmlType;
  25
  26 import eu.etaxonomy.cdm.model.agent.Address;
  27 import eu.etaxonomy.cdm.model.agent.AgentBase;
  28 import eu.etaxonomy.cdm.model.agent.Contact;
  29 import eu.etaxonomy.cdm.model.agent.Institution;
  30 import eu.etaxonomy.cdm.model.agent.InstitutionalMembership;
  31 import eu.etaxonomy.cdm.model.agent.Person;
  32 import eu.etaxonomy.cdm.model.agent.Team;
  33 import eu.etaxonomy.cdm.model.common.AnnotationType;
  34 import eu.etaxonomy.cdm.model.common.ExtensionType;
  35 import eu.etaxonomy.cdm.model.common.Language;
  36 import eu.etaxonomy.cdm.model.common.LanguageString;
  37 import eu.etaxonomy.cdm.model.common.LanguageStringBase;
  38 import eu.etaxonomy.cdm.model.common.MarkerType;
  39 import eu.etaxonomy.cdm.model.common.ReferencedEntityBase;
  40 import eu.etaxonomy.cdm.model.common.RelationshipBase;
  41 import eu.etaxonomy.cdm.model.common.SourcedEntityBase;
  42 import eu.etaxonomy.cdm.model.common.VersionableEntity;
  43 import eu.etaxonomy.cdm.model.description.Feature;
  44 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  45 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  46 import eu.etaxonomy.cdm.model.description.State;
  47 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  48 import eu.etaxonomy.cdm.model.description.TextFormat;
  49 import eu.etaxonomy.cdm.model.location.Country;
  50 import eu.etaxonomy.cdm.model.location.NamedArea;
  51 import eu.etaxonomy.cdm.model.location.NamedAreaLevel;
  52 import eu.etaxonomy.cdm.model.location.NamedAreaType;
  53 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  54 import eu.etaxonomy.cdm.model.media.RightsType;
  55 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  56 import eu.etaxonomy.cdm.model.name.HomotypicalGroup;
  57 import eu.etaxonomy.cdm.model.name.HybridRelationship;
  58 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
  59 import eu.etaxonomy.cdm.model.name.NameRelationship;
  60 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  61 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
  62 import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
  63 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  64 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  65 import eu.etaxonomy.cdm.model.name.Rank;
  66 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
  67 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  68 import eu.etaxonomy.cdm.model.name.TaxonName;
  69 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  70 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
  71 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
  72 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
  73 import eu.etaxonomy.cdm.model.reference.Reference;
  74 import eu.etaxonomy.cdm.model.taxon.Synonym;
  75 import eu.etaxonomy.cdm.model.taxon.SynonymType;
  76 import eu.etaxonomy.cdm.model.taxon.Taxon;
  77 import eu.etaxonomy.cdm.model.taxon.TaxonBase;
  78 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
  79 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
  80 import eu.etaxonomy.cdm.model.term.DefinedTerm;
  81 import eu.etaxonomy.cdm.model.term.DefinedTermBase;
  82 import eu.etaxonomy.cdm.model.term.TermTreeNode;
  83 import eu.etaxonomy.cdm.model.term.TermTree;
  84 import eu.etaxonomy.cdm.model.term.Representation;
  85 import eu.etaxonomy.cdm.model.term.TermVocabulary;
  86
  87 /**
  88  * @author a.babadshanjan
  89  */
  90 @XmlAccessorType(XmlAccessType.FIELD)
  91 @XmlType(name = "", propOrder = {
  92             "terms",
  93             "termVocabularies",
  94                 "agents",
  95                 "agentData",
  96                 "occurrences",
  97             "references",
  98             "referencedEntities",
  99             "featureData",
 100             "languageData",
 101             "taxonomicNames",
 102             "homotypicalGroups",
 103             "taxa",
 104             "synonyms",
 105             "relationships",
 106             "media"
 107 })
 108 @XmlRootElement(name = "DataSet", namespace = "http://etaxonomy.eu/cdm/model/1.0")
 109 public class SDDDataSet {
 110
 111     // Some fields are of type List and some are of type Set.
 112         // This is mainly because
 113         // the service classes return lists, i.e.
 114     // TaxonServiceImpl.getRootTaxa() returns List<Taxon>
 115         // and the Taxon methods return sets, i.e.
 116     // Taxon.getTaxonomicChildren() returns Set<Taxon>.
 117
 118     @XmlElementWrapper(name = "Agents")
 119     @XmlElements({
 120         @XmlElement(name = "Team", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Team.class),
 121         @XmlElement(name = "Institution", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Institution.class),
 122         @XmlElement(name = "Person", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Person.class)
 123     })
 124     protected List<? extends AgentBase> agents;
 125
 126     @XmlElementWrapper(name = "AgentData")
 127     @XmlElements({
 128         @XmlElement(name = "Address", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Address.class),
 129         @XmlElement(name = "Contact", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = Contact.class),
 130         @XmlElement(name = "InstitutionalMembership", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = InstitutionalMembership.class)
 131     })
 132     protected List<VersionableEntity> agentData;
 133
 134     @XmlElementWrapper(name = "FeatureData")
 135         @XmlElements({
 136         @XmlElement(name = "FeatureNode", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TermTreeNode.class),
 137         @XmlElement(name = "FeatureTree", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TermTree.class)
 138     })
 139 //    protected List<VersionableEntity> featureData;
 140     protected List<VersionableEntity> featureData;
 141
 142     @XmlElementWrapper(name = "LanguageData")
 143         @XmlElements({
 144         @XmlElement(name = "Representation", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Representation.class),
 145         @XmlElement(name = "LanguageString", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = LanguageString.class)
 146     })
 147     protected List<LanguageStringBase> languageData;
 148
 149     @XmlElementWrapper(name = "Terms")
 150     @XmlElements({
 151         @XmlElement(name = "AnnotationType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = AnnotationType.class),
 152         @XmlElement(name = "Continent", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
 153         @XmlElement(name = "DerivationEventType", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DerivationEventType.class),
 154         @XmlElement(name = "DeterminationModifier", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DefinedTerm.class),
 155         @XmlElement(name = "ExtensionType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = ExtensionType.class),
 156         @XmlElement(name = "Feature", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = Feature.class),
 157         @XmlElement(name = "HybridRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationshipType.class),
 158         @XmlElement(name = "InstitutionType", namespace = "http://etaxonomy.eu/cdm/model/agent/1.0", type = DefinedTerm.class),
 159         @XmlElement(name = "Language", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = Language.class),
 160         @XmlElement(name = "MarkerType", namespace = "http://etaxonomy.eu/cdm/model/common/1.0", type = MarkerType.class),
 161         @XmlElement(name = "MeasurementUnit", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = MeasurementUnit.class),
 162         @XmlElement(name = "Modifier", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
 163         @XmlElement(name = "NamedArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedArea.class),
 164         @XmlElement(name = "NamedAreaLevel", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaLevel.class),
 165         @XmlElement(name = "NamedAreaType", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = NamedAreaType.class),
 166         @XmlElement(name = "NameRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationshipType.class),
 167         @XmlElement(name = "NomenclaturalCode", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalCode.class),
 168         @XmlElement(name = "NomenclaturalStatusType", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatusType.class),
 169         @XmlElement(name = "PresenceAbsenceTerm", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = PresenceAbsenceTerm.class),
 170         @XmlElement(name = "PreservationMethod", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = PreservationMethod.class),
 171         @XmlElement(name = "Rank", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = Rank.class),
 172         @XmlElement(name = "ReferenceSystem", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = ReferenceSystem.class),
 173         @XmlElement(name = "RightsType", namespace = "http://etaxonomy.eu/cdm/model/media/1.0", type = RightsType.class),
 174         @XmlElement(name = "Scope", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
 175         @XmlElement(name = "Sex", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
 176         @XmlElement(name = "Stage", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = DefinedTerm.class),
 177         @XmlElement(name = "State", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = State.class),
 178         @XmlElement(name = "StatisticalMeasure", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = StatisticalMeasure.class),
 179         @XmlElement(name = "SynonymType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = SynonymType.class),
 180         @XmlElement(name = "TaxonRelationshipType", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationshipType.class),
 181         @XmlElement(name = "TextFormat", namespace = "http://etaxonomy.eu/cdm/model/description/1.0", type = TextFormat.class),
 182         @XmlElement(name = "TypeDesignationStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignationStatus.class),
 183         @XmlElement(name = "Country", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = Country.class)
 184     })
 185     protected List<DefinedTermBase> terms;
 186
 187     @XmlElementWrapper(name = "TermVocabularies")
 188     @XmlElement(name = "TermVocabulary", namespace = "http://etaxonomy.eu/cdm/model/common/1.0")
 189     protected List<TermVocabulary<DefinedTermBase>> termVocabularies;
 190
 191     @XmlElementWrapper(name = "Occurrences")
 192     @XmlElements({
 193         @XmlElement(name = "DnaSample", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = DnaSample.class),
 194         @XmlElement(name = "FieldUnit", namespace = "http://etaxonomy.eu/cdm/model/occurrence/1.0", type = FieldUnit.class)
 195     })
 196     protected List<SpecimenOrObservationBase> occurrences;
 197
 198     @XmlElementWrapper(name = "References")
 199         @XmlElement(name = "Reference", namespace = "http://etaxonomy.eu/cdm/model/reference/1.0", type = Reference.class)
 200
 201     protected List<Reference> references;
 202
 203     @XmlElementWrapper(name = "ReferencedEntities")
 204     @XmlElements({
 205         @XmlElement(name = "NomenclaturalStatus", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NomenclaturalStatus.class),
 206     })
 207     protected List<ReferencedEntityBase> referencedEntities;
 208
 209     @XmlElementWrapper(name = "SourcedEntities")
 210     @XmlElements({
 211         @XmlElement(name = "NameTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameTypeDesignation.class),
 212         @XmlElement(name = "SpecimenTypeDesignation", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = SpecimenTypeDesignation.class)
 213     })
 214     protected List<SourcedEntityBase> sourcedEntities;
 215
 216
 217     @XmlElementWrapper(name = "TaxonomicNames")
 218     @XmlElements({
 219         @XmlElement(name = "TaxonName", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = TaxonName.class),
 220     })
 221     protected List<TaxonName> taxonomicNames;
 222
 223     @XmlElementWrapper(name = "Taxa")
 224     @XmlElement(name = "Taxon", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
 225     protected List<Taxon> taxa;
 226
 227     @XmlElementWrapper(name = "Synonyms")
 228     @XmlElement(name = "Synonym", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0")
 229     protected List<Synonym> synonyms;
 230
 231     @XmlElementWrapper(name = "Relationships")
 232     @XmlElements({
 233         @XmlElement(name = "TaxonRelationship", namespace = "http://etaxonomy.eu/cdm/model/taxon/1.0", type = TaxonRelationship.class),
 234         @XmlElement(name = "NameRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = NameRelationship.class),
 235         @XmlElement(name = "HybridRelationship", namespace = "http://etaxonomy.eu/cdm/model/name/1.0", type = HybridRelationship.class)
 236     })
 237     protected Set<RelationshipBase> relationships;
 238
 239     @XmlElementWrapper(name = "Media_")
 240     @XmlElement(name = "Media", namespace = "http://etaxonomy.eu/cdm/model/media/1.0")
 241     protected List<VersionableEntity> media;
 242
 243     @XmlElementWrapper(name = "HomotypicalGroups")
 244     @XmlElement(name = "HomotypicalGroup", namespace = "http://etaxonomy.eu/cdm/model/name/1.0")
 245     protected List<HomotypicalGroup> homotypicalGroups;
 246
 247 //      @XmlElement(name = "TdwgArea", namespace = "http://etaxonomy.eu/cdm/model/location/1.0", type = TdwgArea.class),
 248
 249         public SDDDataSet () {
 250
 251                 agents = new ArrayList<>();
 252                 agentData = new ArrayList<>();
 253                 featureData = new ArrayList<>();
 254                 languageData = new ArrayList<>();
 255                 terms = new ArrayList<>();
 256                 termVocabularies = new ArrayList<>();
 257                 occurrences = new ArrayList<>();
 258                 references = new ArrayList<>();
 259                 referencedEntities = new ArrayList<>();
 260                 taxonomicNames = new ArrayList<>();
 261                 taxa = new ArrayList<>();
 262                 synonyms = new ArrayList<>();
 263                 media = new ArrayList<>();
 264                 homotypicalGroups = new ArrayList<>();
 265         }
 266
 267     public List<? extends AgentBase> getAgents() {
 268         return agents;
 269     }
 270     public void setAgents(List<? extends AgentBase> value) {
 271         this.agents = value;
 272     }
 273
 274
 275     public List<VersionableEntity> getAgentData() {
 276         return agentData;
 277     }
 278     public void setAgentData(List<VersionableEntity> value) {
 279         this.agentData = value;
 280     }
 281
 282     //public List<? extends TermBase> getTerms() {
 283     public List<DefinedTermBase> getTerms() {
 284         return terms;
 285     }
 286
 287     //public void setTerms(List<? extends TermBase> value) {
 288     public void setTerms(List<DefinedTermBase> value) {
 289         this.terms = value;
 290     }
 291
 292     public List<TermVocabulary<DefinedTermBase>> getTermVocabularies() {
 293         return termVocabularies;
 294     }
 295
 296     public void setTermVocabularies(List<TermVocabulary<DefinedTermBase>> value) {
 297         this.termVocabularies = value;
 298     }
 299
 300     public List<TaxonName> getTaxonomicNames() {
 301         return taxonomicNames;
 302     }
 303     public void setTaxonomicNames(List<TaxonName> value) {
 304         this.taxonomicNames = value;
 305     }
 306
 307     public List<SpecimenOrObservationBase> getOccurrences() {
 308         return occurrences;
 309     }
 310
 311     public void setOccurrences(List<SpecimenOrObservationBase> value) {
 312         this.occurrences = value;
 313     }
 314
 315     public List<Reference> getReferences() {
 316         return references;
 317     }
 318     public void setReferences(List<Reference> value) {
 319         this.references = value;
 320     }
 321
 322     public <T extends ReferencedEntityBase> void addReferencedEntities(Collection<T> value) {
 323         for (T referencedEntity: value) {
 324                 this.referencedEntities.add(referencedEntity);
 325         }
 326     }
 327     public List<ReferencedEntityBase> getReferencedEntities() {
 328         return referencedEntities;
 329     }
 330     public void setReferencedEntities(List<? extends ReferencedEntityBase> value) {
 331         this.referencedEntities = new ArrayList<>();
 332         referencedEntities.addAll(value);
 333     }
 334
 335     public <T extends SourcedEntityBase> void addSourcedEntities(Collection<T> value) {
 336         if (sourcedEntities == null){
 337             this.sourcedEntities = new ArrayList<>();
 338         }
 339         for (T sourcedEntity: value) {
 340             this.sourcedEntities.add(sourcedEntity);
 341         }
 342     }
 343
 344     public List<SourcedEntityBase> getSourcedEntities() {
 345         return sourcedEntities;
 346     }
 347     public void setSourcedEntities(List<? extends SourcedEntityBase> value) {
 348         this.sourcedEntities = new ArrayList<>();
 349         sourcedEntities.addAll(value);
 350     }
 351
 352     public <T extends VersionableEntity> void addFeatureData(Collection<T> value) {
 353         for (T featureItem: value) {
 354                 this.featureData.add(featureItem);
 355         }
 356     }
 357 //    public List<VersionableEntity> getFeatureData() {
 358     public List<VersionableEntity> getFeatureData() {
 359         return featureData;
 360     }
 361     public <T extends VersionableEntity> void setFeatureData(List<T> value) {
 362         featureData = new ArrayList<>();
 363         for (T featureItem: value) {
 364                 this.featureData.add(featureItem);
 365         }
 366     }
 367
 368 //    public void setFeatureData(List<? extends VersionableEntity> value) {
 369     //public void setFeatureData(List<? extends VersionableEntity<?>> value) {
 370 //        this.featureData = new ArrayList<VersionableEntity>();
 371     //    this.featureData = new ArrayList<VersionableEntity<?>>();
 372     //    featureData.addAll(value);
 373     //}
 374
 375     public <T extends LanguageStringBase> void addLanguageData(Collection<T> value) {
 376         for (T languageItem: value) {
 377                 this.languageData.add(languageItem);
 378         }
 379     }
 380     public List<LanguageStringBase> getLanguageData() {
 381         return languageData;
 382     }
 383     public void setLanguageData(List<? extends LanguageStringBase> value) {
 384         this.languageData = new ArrayList<>();
 385         languageData.addAll(value);
 386     }
 387
 388     public void addTaxa(Collection<Taxon> value) {
 389         for (Taxon taxon: value) {
 390                 this.taxa.add(taxon);
 391         }
 392     }
 393
 394     public Collection<? extends TaxonBase> getTaxa() {
 395
 396         //TODO can be deleted when everything works
 397         //Object obj = taxa;
 398         //Collection<TaxonBase> taxonBases = (Collection<TaxonBase>)obj;
 399         List<Taxon> list = taxa;
 400         return list;
 401     }
 402
 403     public Collection<TaxonBase> getTaxonBases() {
 404
 405         Collection<TaxonBase> result = new HashSet<>();
 406         if (taxa != null) {
 407                 result.addAll(taxa);
 408         }
 409         if (synonyms != null) {
 410                 result.addAll(synonyms);
 411         }
 412         return result;
 413     }
 414
 415     public void setTaxa(List<Taxon> value) {
 416         this.taxa = value;
 417     }
 418     public void addTaxon(Taxon value) {
 419                 this.taxa.add(value);
 420     }
 421
 422     public List<Synonym> getSynonyms() {
 423         return synonyms;
 424     }
 425     public void setSynonyms(List<Synonym> value) {
 426         this.synonyms = value;
 427     }
 428
 429     public void addSynonym(Synonym value) {
 430                 this.synonyms.add(value);
 431     }
 432     public void addSynonyms(Collection<Synonym> value) {
 433         for (Synonym synonym: value) {
 434                 this.synonyms.add(synonym);
 435         }
 436     }
 437
 438     public <T extends VersionableEntity> void addMedia(Collection<T> value) {
 439         for (T medium: value) {
 440                 this.media.add(medium);
 441         }
 442     }
 443
 444     public List<VersionableEntity> getMedia() {
 445         return media;
 446     }
 447
 448     public void setMedia(List<? extends VersionableEntity> value) {
 449         this.media = new ArrayList<>();
 450         media.addAll(value);
 451     }
 452
 453     public List<HomotypicalGroup> getHomotypicalGroups() {
 454         return homotypicalGroups;
 455     }
 456
 457     public void setHomotypicalGroups(List<HomotypicalGroup> value) {
 458         this.homotypicalGroups = value;
 459     }
 460
 461 }