cdmlib-persistence/src/main/java/eu/etaxonomy/cdm/database/data/FullCoverageDataGenerator.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.database.data;
   5
   6 import java.net.URI;
   7 import java.util.ArrayList;
   8 import java.util.List;
   9
  10 import org.hibernate.Session;
  11 import org.joda.time.DateTime;
  12
  13 import com.ibm.lsid.MalformedLSIDException;
  14
  15 import eu.etaxonomy.cdm.common.DOI;
  16 import eu.etaxonomy.cdm.model.agent.Address;
  17 import eu.etaxonomy.cdm.model.agent.Contact;
  18 import eu.etaxonomy.cdm.model.agent.Institution;
  19 import eu.etaxonomy.cdm.model.agent.Person;
  20 import eu.etaxonomy.cdm.model.agent.Team;
  21 import eu.etaxonomy.cdm.model.common.AnnotatableEntity;
  22 import eu.etaxonomy.cdm.model.common.Annotation;
  23 import eu.etaxonomy.cdm.model.common.CdmBase;
  24 import eu.etaxonomy.cdm.model.common.Credit;
  25 import eu.etaxonomy.cdm.model.common.DefinedTerm;
  26 import eu.etaxonomy.cdm.model.common.EventBase;
  27 import eu.etaxonomy.cdm.model.common.Extension;
  28 import eu.etaxonomy.cdm.model.common.ExtensionType;
  29 import eu.etaxonomy.cdm.model.common.Group;
  30 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  31 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  32 import eu.etaxonomy.cdm.model.common.Identifier;
  33 import eu.etaxonomy.cdm.model.common.IntextReference;
  34 import eu.etaxonomy.cdm.model.common.LSID;
  35 import eu.etaxonomy.cdm.model.common.LSIDAuthority;
  36 import eu.etaxonomy.cdm.model.common.Language;
  37 import eu.etaxonomy.cdm.model.common.LanguageString;
  38 import eu.etaxonomy.cdm.model.common.Marker;
  39 import eu.etaxonomy.cdm.model.common.MarkerType;
  40 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  41 import eu.etaxonomy.cdm.model.common.Representation;
  42 import eu.etaxonomy.cdm.model.common.TermType;
  43 import eu.etaxonomy.cdm.model.common.TermVocabulary;
  44 import eu.etaxonomy.cdm.model.common.User;
  45 import eu.etaxonomy.cdm.model.description.CategoricalData;
  46 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  47 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  48 import eu.etaxonomy.cdm.model.description.Distribution;
  49 import eu.etaxonomy.cdm.model.description.Feature;
  50 import eu.etaxonomy.cdm.model.description.FeatureNode;
  51 import eu.etaxonomy.cdm.model.description.FeatureTree;
  52 import eu.etaxonomy.cdm.model.description.IIdentificationKey;
  53 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  54 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  55 import eu.etaxonomy.cdm.model.description.MediaKey;
  56 import eu.etaxonomy.cdm.model.description.MultiAccessKey;
  57 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  58 import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
  59 import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
  60 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  61 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  62 import eu.etaxonomy.cdm.model.description.State;
  63 import eu.etaxonomy.cdm.model.description.StateData;
  64 import eu.etaxonomy.cdm.model.description.StatisticalMeasure;
  65 import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue;
  66 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  67 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  68 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  69 import eu.etaxonomy.cdm.model.description.TextData;
  70 import eu.etaxonomy.cdm.model.description.TextFormat;
  71 import eu.etaxonomy.cdm.model.description.WorkingSet;
  72 import eu.etaxonomy.cdm.model.location.Country;
  73 import eu.etaxonomy.cdm.model.location.NamedArea;
  74 import eu.etaxonomy.cdm.model.location.Point;
  75 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  76 import eu.etaxonomy.cdm.model.media.AudioFile;
  77 import eu.etaxonomy.cdm.model.media.IdentifiableMediaEntity;
  78 import eu.etaxonomy.cdm.model.media.ImageFile;
  79 import eu.etaxonomy.cdm.model.media.Media;
  80 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  81 import eu.etaxonomy.cdm.model.media.MovieFile;
  82 import eu.etaxonomy.cdm.model.media.Rights;
  83 import eu.etaxonomy.cdm.model.media.RightsType;
  84 import eu.etaxonomy.cdm.model.molecular.Amplification;
  85 import eu.etaxonomy.cdm.model.molecular.AmplificationResult;
  86 import eu.etaxonomy.cdm.model.molecular.Cloning;
  87 import eu.etaxonomy.cdm.model.molecular.DnaQuality;
  88 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  89 import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;
  90 import eu.etaxonomy.cdm.model.molecular.Primer;
  91 import eu.etaxonomy.cdm.model.molecular.Sequence;
  92 import eu.etaxonomy.cdm.model.molecular.SequenceDirection;
  93 import eu.etaxonomy.cdm.model.molecular.SequenceString;
  94 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  95 import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
  96 import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment.Shift;
  97 import eu.etaxonomy.cdm.model.name.BacterialName;
  98 import eu.etaxonomy.cdm.model.name.BotanicalName;
  99 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
 100 import eu.etaxonomy.cdm.model.name.HybridRelationship;
 101 import eu.etaxonomy.cdm.model.name.HybridRelationshipType;
 102 import eu.etaxonomy.cdm.model.name.NameRelationship;
 103 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
 104 import eu.etaxonomy.cdm.model.name.NameTypeDesignation;
 105 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
 106 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
 107 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
 108 import eu.etaxonomy.cdm.model.name.Rank;
 109 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
 110 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
 111 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
 112 import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
 113 import eu.etaxonomy.cdm.model.name.ViralName;
 114 import eu.etaxonomy.cdm.model.name.ZoologicalName;
 115 import eu.etaxonomy.cdm.model.occurrence.Collection;
 116 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
 117 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
 118 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
 119 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
 120 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 121 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
 122 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
 123 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 124 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
 125 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 126 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 127 import eu.etaxonomy.cdm.model.reference.Reference;
 128 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
 129 import eu.etaxonomy.cdm.model.taxon.Classification;
 130 import eu.etaxonomy.cdm.model.taxon.Synonym;
 131 import eu.etaxonomy.cdm.model.taxon.SynonymType;
 132 import eu.etaxonomy.cdm.model.taxon.Taxon;
 133 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
 134 import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
 135 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 136 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
 137
 138 /**
 139  * This class tries to create a database that has
 140  * at least one record in each table.
 141  * It is meant to test update scripts as well as imports
 142  * and exports.
 143  *
 144  * ATTENTION: As the content of the created database may change
 145  * over time due to model changes and other requirements test using
 146  * this class should be written in a way that they do rather
 147  * depend on general parameter than concrete data values.
 148  *
 149  * @author a.mueller
 150  * @created 3013-12-02
 151  *
 152  *
 153  */
 154 public class FullCoverageDataGenerator {
 155
 156
 157         public void fillWithData(Session session){
 158                 List<CdmBase> cdmBases = new ArrayList<CdmBase>();
 159
 160                 createAgents(cdmBases);
 161
 162                 createDescriptions(cdmBases);
 163
 164                 createMedia(cdmBases);
 165
 166                 createMolecular(cdmBases);
 167
 168                 createTaxonName(cdmBases);
 169
 170                 createOccurrence(cdmBases);
 171
 172                 createReference(cdmBases);
 173
 174                 createTaxon(cdmBases);
 175
 176                 createSupplemental(cdmBases);
 177
 178                 for (CdmBase cdmBase: cdmBases){
 179                         session.save(cdmBase);
 180                 }
 181         }
 182
 183
 184         private void createSupplemental(List<CdmBase> cdmBases)  {
 185
 186                 Reference ref = ReferenceFactory.newBook();
 187
 188                 Annotation annotation = Annotation.NewDefaultLanguageInstance("annotation");
 189                 ref.addAnnotation(annotation);
 190                 handleAnnotatableEntity(annotation);
 191
 192                 Credit credit = Credit.NewInstance(Person.NewInstance(), "refCredit", "rc", Language.DEFAULT());
 193                 ref.addCredit(credit);
 194                 handleAnnotatableEntity(credit);
 195
 196                 Rights rights = Rights.NewInstance("My rights", Language.GERMAN());
 197                 ref.addRights(rights);
 198                 handleAnnotatableEntity(rights);
 199
 200                 //Others
 201                 try {
 202                         LSIDAuthority lsidAuthority = new LSIDAuthority("My authority");
 203                         lsidAuthority.addNamespace("lsidNamespace", TaxonNameBase.class);
 204                         cdmBases.add(lsidAuthority);
 205                 } catch (MalformedLSIDException e) {
 206                         e.printStackTrace();
 207                 }
 208
 209                 User user = User.NewInstance("myUser", "12345");
 210                 Group group = Group.NewInstance("MyGroup");
 211                 group.addMember(user);
 212
 213                 cdmBases.add(user);
 214                 cdmBases.add(group);
 215
 216
 217                 cdmBases.add(ref);
 218
 219         }
 220
 221
 222         /**
 223          * @param cdmBases
 224          */
 225         private void createAgents(List<CdmBase> cdmBases) {
 226                 //Person
 227                 Person person = Person.NewTitledInstance("Person Title");
 228                 person.setFirstname("first name");
 229                 person.setLastname("last name");
 230                 person.setLifespan(TimePeriodParser.parseString("1905-1995"));
 231                 person.setPrefix("prefix");
 232                 person.setSuffix("suffix");
 233
 234                 handleIdentifiableEntity(person);
 235
 236                 //Contact
 237                 Contact contact = Contact.NewInstance();
 238                 person.setContact(contact);
 239                 Point locality = Point.NewInstance(45.12, -38.69, ReferenceSystem.WGS84(), 22);
 240                 contact.addEmailAddress("a@b.de");
 241                 contact.addFaxNumber("f:010-123456");
 242                 contact.addPhoneNumber("p:090-987654");
 243                 contact.addUrl(URI.create("http://www.abc.de"));
 244
 245                 //Address
 246                 Address address = Address.NewInstance(Country.GERMANY(), "locality", "pobox", "12345", "region", "street", locality);
 247                 contact.addAddress(address);
 248
 249                 //Team
 250                 Team team = Team.NewTitledInstance("Team title", "Team abbrev title");
 251                 team.addTeamMember(person);
 252                 handleIdentifiableEntity(team);
 253
 254
 255                 //Institution
 256                 Institution institution = Institution.NewInstance();
 257                 institution.setCode("institution code");
 258                 institution.setName("institution name");
 259                 handleIdentifiableEntity(institution);
 260
 261
 262                 //TODO vocabulary
 263 //              voc = "29ad808b-3126-4274-be81-4561e7afc76f"
 264                 DefinedTerm instType = DefinedTerm.NewInstitutionTypeInstance("Description forthis instition type", "institution type", "inst. t.");
 265                 cdmBases.add(instType);
 266                 institution.addType(instType);
 267                 person.addInstitutionalMembership(institution, TimePeriodParser.parseString("1955-1956"), "department", "role");
 268
 269                 Institution subInstitution = Institution.NewInstance();
 270                 subInstitution.setCode("sub institution code");
 271                 subInstitution.setName("sub institution name");
 272                 subInstitution.setIsPartOf(institution);
 273
 274                 cdmBases.add(person);
 275                 cdmBases.add(team);
 276                 cdmBases.add(institution);
 277         }
 278
 279
 280         private void createDescriptions(List<CdmBase> cdmBases) {
 281
 282                 TermVocabulary<?> voc = TermVocabulary.NewInstance(TermType.AnnotationType, "my termVoc desc",
 283                                 "myTerm voc", "mtv", URI.create("http://www.abc.de"));
 284                 handleIdentifiableEntity(voc);
 285                 cdmBases.add(voc);
 286
 287                 Representation rep = voc.getRepresentations().iterator().next();
 288                 handleAnnotatableEntity(rep);
 289 //              Representation engRep = Language.ENGLISH().getRepresentations().iterator().next();
 290 //              handleAnnotatableEntity(engRep);
 291 //              cdmBases.add(engRep);  //needed?
 292
 293                 //Categorical data
 294                 State state = State.NewInstance("Test state", "state", "st.");
 295                 state.addMedia(Media.NewInstance());
 296                 cdmBases.add(state);
 297                 CategoricalData categoricalData = CategoricalData.NewInstance(state, Feature.CONSERVATION());
 298                 StateData stateData = categoricalData.getStateData().get(0);
 299                 stateData.addModifier(DefinedTerm.SEX_FEMALE());
 300                 handleAnnotatableEntity(categoricalData);
 301
 302
 303                 State nextState = State.NewInstance();
 304                 cdmBases.add(nextState);
 305                 StateData stateData2 = StateData.NewInstance(nextState);
 306                 stateData2.putModifyingText(Language.ENGLISH(), "State2 modifying text");
 307                 categoricalData.addStateData(stateData2);
 308                 categoricalData.setOrderRelevant(true);
 309
 310                 //Quantitative data
 311                 Feature leaveLength = Feature.NewInstance("Leave length description", "leave length", "l.l.");
 312                 cdmBases.add(leaveLength);
 313                 leaveLength.setSupportsQuantitativeData(true);
 314                 QuantitativeData quantitativeData = QuantitativeData.NewInstance(leaveLength);
 315                 MeasurementUnit measurementUnit = MeasurementUnit.NewInstance("Measurement Unit", "munit", null);
 316                 cdmBases.add(measurementUnit);
 317                 quantitativeData.setUnit(measurementUnit);
 318                 StatisticalMeasurementValue statisticalMeasurementValue = quantitativeData.setAverage((float)22.9 , null);
 319                 handleAnnotatableEntity(quantitativeData);
 320                 handleIdentifiableEntity(measurementUnit);
 321                 DefinedTerm valueModifier = DefinedTerm.NewModifierInstance("about", "about", null);
 322                 statisticalMeasurementValue.addModifier(valueModifier);
 323                 cdmBases.add(valueModifier);
 324
 325                 //Feature
 326                 TermVocabulary<DefinedTerm> recommendedModifierEnumeration = TermVocabulary.NewInstance(TermType.Modifier, DefinedTerm.class);
 327                 leaveLength.addRecommendedModifierEnumeration(recommendedModifierEnumeration);
 328                 cdmBases.add(recommendedModifierEnumeration);
 329                 TermVocabulary<State> supportedCategoricalEnumeration = TermVocabulary.NewInstance(TermType.State, State.class);
 330                 leaveLength.addSupportedCategoricalEnumeration(supportedCategoricalEnumeration);
 331                 cdmBases.add(supportedCategoricalEnumeration);
 332                 leaveLength.addRecommendedMeasurementUnit(measurementUnit);
 333                 leaveLength.addRecommendedStatisticalMeasure(StatisticalMeasure.AVERAGE());
 334
 335                 CommonTaxonName commonTaxonName = CommonTaxonName.NewInstance("common name", Language.ENGLISH(), Country.UNITEDSTATESOFAMERICA());
 336                 handleAnnotatableEntity(commonTaxonName);
 337
 338                 TextData textData = TextData.NewInstance(Feature.DIAGNOSIS());
 339                 Language eng = Language.ENGLISH();
 340                 textData.putText(eng, "My text data");
 341                 LanguageString languageString = textData.getLanguageText(eng);
 342
 343                 Taxon referencedTaxon = getTaxon();
 344                 cdmBases.add(referencedTaxon);
 345                 languageString.addIntextReference(IntextReference.NewTaxonInstance(referencedTaxon, languageString, 2, 5));
 346                 textData.putModifyingText(eng, "nice diagnosis");
 347                 handleAnnotatableEntity(textData);
 348                 handleAnnotatableEntity(languageString);
 349
 350                 TextFormat format = TextFormat.NewInstance("format", "format", null);
 351                 textData.setFormat(format);
 352                 cdmBases.add(format);
 353                 handleAnnotatableEntity(format);
 354
 355                 DerivedUnit specimen = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 356                 IndividualsAssociation indAssoc = IndividualsAssociation.NewInstance(specimen);
 357                 indAssoc.putDescription(Language.ENGLISH(), "description for individuals association");
 358                 handleAnnotatableEntity(indAssoc);
 359
 360
 361                 TaxonInteraction taxonInteraction = TaxonInteraction.NewInstance(Feature.HOSTPLANT());
 362                 taxonInteraction.putDescription(Language.ENGLISH(), "interaction description");
 363                 handleAnnotatableEntity(taxonInteraction);
 364
 365                 NamedArea inCountryArea = NamedArea.NewInstance("My area in a country", "my area", "ma");
 366                 inCountryArea.addCountry(Country.TURKEYREPUBLICOF());
 367                 cdmBases.add(inCountryArea);
 368                 Distribution distribution = Distribution.NewInstance(inCountryArea, PresenceAbsenceTerm.CULTIVATED());
 369                 handleAnnotatableEntity(distribution);
 370
 371                 Taxon taxon = getTaxon();
 372                 TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
 373                 taxonDescription.addElements(categoricalData, quantitativeData,
 374                                 textData, commonTaxonName, taxonInteraction, indAssoc, distribution);
 375
 376                 DerivedUnit describedSpecimenOrObservation = DerivedUnit.NewInstance(SpecimenOrObservationType.DerivedUnit);
 377                 taxonDescription.setDescribedSpecimenOrObservation(describedSpecimenOrObservation);
 378
 379                 taxonDescription.addScope(DefinedTerm.SEX_FEMALE());
 380                 taxonDescription.addGeoScope(Country.GERMANY());
 381                 handleIdentifiableEntity(taxonDescription);
 382
 383                 cdmBases.add(taxon);
 384
 385                 //DescriptionElmenetBase  + source
 386                 textData.addMedia(Media.NewInstance());
 387                 textData.addModifier(DefinedTerm.SEX_HERMAPHRODITE());
 388                 textData.putModifyingText(Language.ENGLISH(), "no modification");
 389                 textData.setTimeperiod(TimePeriodParser.parseString("1970-1980"));
 390                 Reference ref = ReferenceFactory.newArticle();
 391                 DescriptionElementSource source = textData.addSource(OriginalSourceType.Import, "22", "taxon description table", ref, "detail");
 392                 source.setNameUsedInSource(TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()));
 393                 handleAnnotatableEntity(source);
 394
 395                 taxonDescription.addDescriptionSource(ref);
 396
 397
 398                 //Specimen description
 399                 SpecimenOrObservationBase<?> describedSpecimen = getSpecimen();
 400                 SpecimenDescription specDesc = SpecimenDescription.NewInstance(specimen);
 401                 cdmBases.add(describedSpecimen);
 402                 handleAnnotatableEntity(specDesc);
 403
 404                 //Name description
 405                 TaxonNameBase<?,?> name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
 406                 TaxonNameDescription nameDesc = TaxonNameDescription.NewInstance(name);
 407                 cdmBases.add(name);
 408                 handleAnnotatableEntity(nameDesc);
 409
 410
 411                 //Feature Tree
 412                 FeatureTree featureTree = FeatureTree.NewInstance();
 413 //              featureTree
 414                 FeatureNode descriptionFeatureNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 415                 FeatureNode leaveLengthNode = FeatureNode.NewInstance(leaveLength);
 416                 featureTree.getRootChildren().add(descriptionFeatureNode);
 417                 descriptionFeatureNode.addChild(leaveLengthNode);
 418                 handleIdentifiableEntity(featureTree);
 419
 420                 State inapplicableState = State.NewInstance("inapplicableState", "inapplicableState", null);
 421                 State applicableState = State.NewInstance("only applicable state", "only applicable state", null);
 422                 cdmBases.add(applicableState);
 423                 cdmBases.add(inapplicableState);
 424                 leaveLengthNode.addInapplicableState(inapplicableState);
 425                 leaveLengthNode.addApplicableState(applicableState);
 426                 cdmBases.add(featureTree);
 427                 cdmBases.add(leaveLengthNode);
 428
 429
 430                 WorkingSet workingSet = WorkingSet.NewInstance();
 431                 workingSet.addDescription(taxonDescription);
 432                 workingSet.setLabel("My Workingset");
 433                 workingSet.getDescriptiveSystem();
 434                 handleAnnotatableEntity(workingSet);
 435
 436
 437                 //polytomous keys
 438                 Taxon coveredTaxon = Taxon.NewInstance(name, null);
 439                 PolytomousKey key = PolytomousKey.NewTitledInstance("My Polykey");
 440                 handleIdentificationKey(key, taxon, coveredTaxon);
 441                 key.setStartNumber(10);
 442
 443
 444                 PolytomousKeyNode firstChildNode = PolytomousKeyNode.NewInstance("Green", "What is the leave length?", coveredTaxon, leaveLength);
 445                 key.getRoot().addChild(firstChildNode);
 446                 PolytomousKeyNode secondChildNode = PolytomousKeyNode.NewInstance("234");
 447                 firstChildNode.addChild(secondChildNode);
 448
 449                 PolytomousKey subkey = PolytomousKey.NewTitledInstance("Sub-key");
 450                 firstChildNode.setSubkey(subkey);
 451
 452                 PolytomousKeyNode subKeyNode = PolytomousKeyNode.NewInstance("sub key couplet");
 453                 subkey.getRoot().addChild(subKeyNode);
 454                 secondChildNode.setOtherNode(subKeyNode);
 455
 456                 secondChildNode.putModifyingText(Language.GERMAN(), "manchmal");
 457
 458                 cdmBases.add(key);
 459                 cdmBases.add(subkey);
 460
 461                 MediaKey mediaKey = MediaKey.NewInstance();
 462                 mediaKey.addKeyRepresentation(Representation.NewInstance("Media Key Representation", "media key", null, Language.ENGLISH()));
 463                 handleIdentificationKey(mediaKey, taxon, coveredTaxon);
 464
 465                 MultiAccessKey multiAccessKey = MultiAccessKey.NewInstance();
 466                 handleIdentificationKey(multiAccessKey, taxon, coveredTaxon);
 467
 468                 cdmBases.add(mediaKey);
 469                 cdmBases.add(multiAccessKey);
 470
 471         }
 472
 473
 474
 475         private void handleIdentificationKey(IIdentificationKey key, Taxon taxon, Taxon coveredTaxon){
 476                 key.addCoveredTaxon(coveredTaxon);
 477                 key.addGeographicalScope(Country.GERMANY());
 478                 key.addScopeRestriction(DefinedTerm.SEX_FEMALE());
 479                 key.addTaxonomicScope(taxon);
 480                 if (key instanceof IdentifiableEntity<?>){
 481                         handleIdentifiableEntity((IdentifiableEntity<?>)key);
 482                 }else{
 483                         handleAnnotatableEntity((AnnotatableEntity)key);
 484                 }
 485
 486
 487         }
 488
 489
 490         private void createMedia(List<CdmBase> cdmBases){
 491                 AudioFile audioFile = AudioFile.NewInstance(URI.create("http://a.b.de"), 22);
 492                 ImageFile imageFile = ImageFile.NewInstance(URI.create("http://b.c.de"), 44, 467, 55);
 493                 MovieFile movieFile = MovieFile.NewInstance(URI.create("http://b.c.de"), 67);
 494                 MediaRepresentation mediaRepresentation = MediaRepresentation.NewInstance("mime", "media");
 495
 496                 mediaRepresentation.addRepresentationPart(movieFile);
 497                 mediaRepresentation.addRepresentationPart(imageFile);
 498                 mediaRepresentation.addRepresentationPart(audioFile);
 499                 Media media = Media.NewInstance();
 500                 media.addRepresentation(mediaRepresentation);
 501
 502                 media.putTitle(Language.ENGLISH(), "Media title");
 503                 media.setMediaCreated(DateTime.now());
 504                 media.putDescription(Language.ENGLISH(), "Media description");
 505                 handleIdentifiableEntity(media);
 506
 507
 508                 Person artist = Person.NewTitledInstance("artist");
 509                 media.setArtist(artist);
 510                 cdmBases.add(media);
 511                 cdmBases.add(artist);
 512         }
 513
 514
 515         private void createMolecular(List<CdmBase> cdmBases) {
 516                 DnaSample dnaSample = DnaSample.NewInstance();
 517
 518                 //Amplification
 519                 Amplification amplification = Amplification.NewInstance();
 520
 521                 DefinedTerm dnaMarker = DefinedTerm.NewDnaMarkerInstance("My dna marker", "dna marker", null);
 522                 cdmBases.add(dnaMarker);
 523                 amplification.setDnaMarker(dnaMarker);
 524                 Institution inst = Institution.NewInstance();
 525                 amplification.setInstitution(inst);
 526                 handleEventBase(amplification);
 527                 handleAnnotatableEntity(amplification);
 528
 529                 Primer forwardPrimer = Primer.NewInstance("forward primer");
 530                 forwardPrimer.setPublishedIn(getReference());
 531                 forwardPrimer.setSequence(SequenceString.NewInstance("my sequence"));
 532                 handleAnnotatableEntity(forwardPrimer);
 533
 534                 Primer reversePrimer = Primer.NewInstance("reverse primer");
 535                 handleAnnotatableEntity(reversePrimer);
 536
 537                 amplification.setForwardPrimer(forwardPrimer);
 538                 amplification.setReversePrimer(reversePrimer);
 539
 540                 DefinedTerm purificationMethod = DefinedTerm.NewInstance(TermType.MaterialOrMethod, "purification method", "purification method", null);
 541                 cdmBases.add(purificationMethod);
 542                 MaterialOrMethodEvent purification = MaterialOrMethodEvent.NewInstance(purificationMethod, "purification method");
 543                 amplification.setPurification(purification);
 544                 handleAnnotatableEntity(purification);
 545                 handleAnnotatableEntity(purificationMethod);
 546
 547                 amplification.setLadderUsed("ladder");
 548                 amplification.setElectrophoresisVoltage(5.5);
 549                 amplification.setGelConcentration(2.4);
 550                 amplification.setGelRunningTime(3.6);
 551
 552                 //Amplification result
 553                 AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample, amplification);
 554                 amplificationResult.setSuccessful(true);
 555                 amplificationResult.setSuccessText("Very successful");
 556                 handleAnnotatableEntity(amplificationResult);
 557
 558                 DefinedTerm cloningMethod = DefinedTerm.NewInstance(TermType.MaterialOrMethod, "cloning method", "cloning method", null);
 559                 cdmBases.add(cloningMethod);
 560                 Cloning cloning = Cloning.NewInstance(cloningMethod, "My cloning method", "my strain", forwardPrimer, reversePrimer);
 561                 amplificationResult.setCloning(cloning);
 562                 handleAnnotatableEntity(cloningMethod);
 563                 handleAnnotatableEntity(cloning);
 564
 565                 Media gelPhoto = Media.NewInstance();
 566                 amplificationResult.setGelPhoto(gelPhoto);
 567
 568                 //SingleRead
 569                 SingleRead singleRead = SingleRead.NewInstance();
 570                 handleAnnotatableEntity(singleRead);
 571                 amplificationResult.addSingleRead(singleRead);
 572                 MaterialOrMethodEvent readMethod = MaterialOrMethodEvent.NewInstance(null, "read method");
 573                 singleRead.setMaterialOrMethod(readMethod);
 574                 handleAnnotatableEntity(readMethod);
 575
 576                 Media pherogram = Media.NewInstance();
 577                 singleRead.setPherogram(pherogram);
 578
 579                 singleRead.setPrimer(forwardPrimer);
 580                 singleRead.setSequence(SequenceString.NewInstance("ABTC"));
 581                 singleRead.setDirection(SequenceDirection.Forward);
 582
 583                 //Sequence
 584                 Sequence sequence = Sequence.NewInstance("ADDT");
 585                 dnaSample.addSequence(sequence);
 586
 587 //              SequenceString alignedSequence = SequenceString.NewInstance("AGTC");
 588                 Shift[] shifts = new Shift[]{new Shift(66,1),new Shift(103,-2)};
 589                 SingleReadAlignment.NewInstance(sequence, singleRead, shifts, "AGTC");
 590
 591                 Media contigFile = Media.NewInstance();
 592                 sequence.setContigFile(contigFile);
 593                 sequence.setIsBarcode(true);
 594                 sequence.setDnaMarker(dnaMarker);
 595                 sequence.setBarcodeSequencePart(SequenceString.NewInstance("ADTA"));
 596                 sequence.setGeneticAccessionNumber("GenNO12345");
 597                 sequence.setBoldProcessId("boldId");
 598                 sequence.setHaplotype("haplotype");
 599                 Reference sequenceCitation = getReference();
 600                 sequence.addCitation(sequenceCitation);
 601                 handleAnnotatableEntity(sequence);
 602
 603                 //DnaQuality
 604                 DnaQuality dnaQuality = DnaQuality.NewInstance();
 605                 dnaQuality.setConcentration(2.0);
 606                 MeasurementUnit mu = MeasurementUnit.NewInstance("mg/ml", "mg/ml","mg/ml");
 607                 cdmBases.add(mu);
 608                 dnaQuality.setConcentrationUnit(mu);
 609                 dnaQuality.setPurificationMethod("purification method");
 610                 dnaQuality.setQualityCheckDate(DateTime.now());
 611                 dnaQuality.setQualityTerm(null); //TODO
 612                 dnaQuality.setRatioOfAbsorbance260_230(22.0);
 613                 dnaQuality.setRatioOfAbsorbance260_280(3.9);
 614                 dnaSample.setDnaQuality(dnaQuality);
 615
 616
 617                 //Phylogenetic Tree
 618                 PhylogeneticTree phyloTree = PhylogeneticTree.NewInstance();
 619                 phyloTree.addUsedSequences(sequence);
 620                 handleIdentifiableEntity(phyloTree);
 621
 622
 623                 cdmBases.add(dnaSample);
 624                 cdmBases.add(phyloTree);
 625         }
 626
 627
 628         private void createTaxon(List<CdmBase> cdmBases) {
 629                 Reference sec = getReference();
 630                 TaxonNameBase<?,?> name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
 631                 Taxon taxon = Taxon.NewInstance(name, sec);
 632                 handleIdentifiableEntity(taxon);
 633
 634                 TaxonNameBase<?,?> synName = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
 635                 Synonym syn = Synonym.NewInstance(synName, sec, "123");
 636                 taxon.addSynonym(syn, SynonymType.HETEROTYPIC_SYNONYM_OF());
 637                 taxon.setDoubtful(true);
 638                 handleIdentifiableEntity(syn);
 639
 640
 641                 Taxon concept = Taxon.NewInstance(name, getReference());
 642                 TaxonRelationship taxRel = taxon.addTaxonRelation(concept, TaxonRelationshipType.CONGRUENT_TO(),
 643                                 sec, "444");
 644                 taxon.setTaxonStatusUnknown(true);
 645                 handleAnnotatableEntity(taxRel);
 646
 647
 648                 //Classification
 649                 Classification classification = Classification.NewInstance("My classification", sec);
 650                 classification.setMicroReference("p. 123");
 651                 classification.setTimeperiod(TimePeriodParser.parseString("1.1.2012-4.8.2013"));
 652                 classification.addGeoScope(Country.GERMANY());
 653                 classification.putDescription(Language.ENGLISH(), "An interesting classification");
 654
 655
 656                 TaxonNode node = classification.addChildTaxon(taxon, sec,"22");
 657                 handleIdentifiableEntity(classification);
 658                 handleAnnotatableEntity(node);
 659
 660                 Taxon childTaxon = Taxon.NewInstance(synName, sec);
 661                 node.addChildTaxon(childTaxon, sec, "44");
 662             node.setUnplaced(true);
 663             node.setExcluded(true);
 664
 665                 cdmBases.add(taxon);
 666                 cdmBases.add(concept);
 667                 cdmBases.add(childTaxon);
 668                 cdmBases.add(classification);
 669
 670
 671         }
 672
 673
 674
 675
 676         private void createReference(List<CdmBase> cdmBases) {
 677                 Reference reference = ReferenceFactory.newArticle();
 678                 Person author = Person.NewTitledInstance("Author team");
 679                 reference.setAuthorship(author);
 680                 reference.setTitle("ref title");
 681                 reference.setAbbrevTitle("abbrev title");
 682                 reference.setDatePublished(TimePeriodParser.parseString("1999"));
 683                 reference.setEdition("edition");
 684                 reference.setEditor("editor");
 685                 Institution institution = Institution.NewInstance();
 686                 reference.setInstitution(institution);
 687                 reference.setIsbn("1234556");
 688                 reference.setIssn("issn");
 689                 reference.setDoi(DOI.fromRegistrantCodeAndSuffix("14356", "suffix"));
 690                 reference.setReferenceAbstract("referenceAbstract");
 691                 reference.setOrganization("organization");
 692                 reference.setPages("123-134");
 693                 reference.setPlacePublished("place Published");
 694                 reference.setPublisher("publisher");
 695                 Institution school = Institution.NewInstance();
 696                 reference.setSchool(school);
 697 //              reference.setSeriesPart("series");
 698                 reference.setSeriesPart("seriesPart");
 699                 reference.setVolume("vol. 3");
 700                 reference.setUri(URI.create("http://rer.abc.de"));
 701
 702                 Reference journal = ReferenceFactory.newJournal();
 703                 reference.setInJournal(journal);
 704
 705                 handleIdentifiableEntity(reference);
 706
 707                 cdmBases.add(reference);
 708
 709         }
 710
 711
 712
 713
 714         private void createOccurrence(List<CdmBase> cdmBases) {
 715                 //Collection
 716                 Collection collection = Collection.NewInstance();
 717                 Collection subCollection = Collection.NewInstance();
 718                 subCollection.setSuperCollection(collection);
 719                 handleIdentifiableEntity(collection);
 720                 handleIdentifiableEntity(subCollection);
 721                 cdmBases.add(subCollection);
 722
 723                 collection.setCode("coll code");
 724                 collection.setCodeStandard("codeStandard");
 725                 collection.setName("coll name");
 726                 collection.setTownOrLocation("townOrLocation");
 727                 Institution institution = Institution.NewInstance();
 728                 collection.setInstitute(institution);
 729
 730                 //FieldUnit
 731                 FieldUnit fieldUnit = FieldUnit.NewInstance();
 732                 fieldUnit.setFieldNumber("fieldNumber");
 733                 fieldUnit.setFieldNotes("fieldNotes");
 734                 Person primaryCollector = Person.NewInstance();
 735                 fieldUnit.setPrimaryCollector(primaryCollector);
 736                 handleIdentifiableEntity(fieldUnit);
 737
 738                 GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
 739                 fieldUnit.setGatheringEvent(gatheringEvent);
 740                 gatheringEvent.putLocality(Language.ENGLISH(), "locality");
 741                 gatheringEvent.setExactLocation(Point.NewInstance(22.4, -34.2,
 742                                 ReferenceSystem.WGS84(), 33));
 743                 gatheringEvent.setCountry(Country.GERMANY());
 744                 gatheringEvent.addCollectingArea(NamedArea.EUROPE());
 745                 gatheringEvent.setCollectingMethod("collectingMethod");
 746                 gatheringEvent.setAbsoluteElevation(10);
 747                 gatheringEvent.setAbsoluteElevationMax(100);
 748                 gatheringEvent.setAbsoluteElevationText("elevation text");
 749
 750                 gatheringEvent.setDistanceToGround(10.4);
 751                 gatheringEvent.setDistanceToGroundMax(100.3);
 752                 gatheringEvent.setDistanceToGroundText("distance to ground text");
 753
 754                 gatheringEvent.setDistanceToWaterSurface(10.4);
 755                 gatheringEvent.setDistanceToWaterSurfaceMax(100.3);
 756                 gatheringEvent.setDistanceToWaterSurfaceText("distance to water text");
 757                 handleAnnotatableEntity(gatheringEvent);
 758                 handleEventBase(gatheringEvent);
 759
 760
 761                 //Derived Unit
 762                 MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
 763                 mediaSpecimen.setCollection(collection);
 764                 mediaSpecimen.setCatalogNumber("catalogNumber");
 765                 mediaSpecimen.setAccessionNumber("accessionNumber");
 766 //              mediaSpecimen.setCollectorsNumber("collectorsNumber");
 767                 mediaSpecimen.setBarcode("barcode");
 768                 BotanicalName storedUnder = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
 769                 storedUnder.setTitleCache("Stored under", true);
 770                 mediaSpecimen.setStoredUnder(storedUnder);
 771                 mediaSpecimen.setExsiccatum("exsiccatum");
 772                 PreservationMethod preservation = PreservationMethod.NewInstance(null, "My preservation");
 773                 preservation.setTemperature(22.4);
 774                 mediaSpecimen.setPreservation(preservation);
 775                 mediaSpecimen.setOriginalLabelInfo("Original Label Info");
 776                 handleIdentifiableEntity(mediaSpecimen);
 777
 778                 //DerivationEvent
 779                 DerivationEvent event = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());
 780                 event.addOriginal(fieldUnit);
 781                 event.addDerivative(mediaSpecimen);
 782                 Institution inst = Institution.NewInstance();
 783                 event.setInstitution(inst);
 784                 handleAnnotatableEntity(event);
 785                 handleEventBase(event);
 786
 787                 //SpecOrObservationBase
 788                 fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
 789                 DefinedTerm lifeStage = DefinedTerm.NewStageInstance("Live stage", "stage", null);
 790                 cdmBases.add(lifeStage);
 791                 fieldUnit.setLifeStage(lifeStage);
 792                 DefinedTerm kindOfUnit = DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null);
 793                 cdmBases.add(kindOfUnit);
 794                 fieldUnit.setKindOfUnit(kindOfUnit);
 795                 fieldUnit.setIndividualCount(3);
 796                 fieldUnit.putDefinition(Language.ENGLISH(), "definition");
 797                 fieldUnit.setPublish(true);
 798                 handleIdentifiableEntity(fieldUnit);
 799
 800                 //Determination
 801                 DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(getTaxon(), mediaSpecimen);
 802                 determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
 803                 determinationEvent.setPreferredFlag(true);
 804                 determinationEvent.addReference(getReference());
 805                 handleAnnotatableEntity(determinationEvent);
 806                 handleEventBase(determinationEvent);
 807
 808                 cdmBases.add(fieldUnit);
 809                 cdmBases.add(mediaSpecimen);
 810                 cdmBases.add(collection);
 811         }
 812
 813
 814         private void createTaxonName(List<CdmBase> cdmBases) {
 815                 BacterialName bacName = TaxonNameFactory.NewBacterialInstance(Rank.GENUS());
 816                 bacName.setSubGenusAuthorship("sub Genus author");
 817                 bacName.setNameApprobation("nameApprobation");
 818                 handleIdentifiableEntity(bacName);
 819
 820                 CultivarPlantName botName = TaxonNameFactory.NewCultivarInstance(Rank.SUBSPECIES());
 821                 botName.setAnamorphic(true);
 822                 botName.setCultivarName("cultivarName");
 823                 botName.setGenusOrUninomial("Genus");
 824                 botName.setInfraGenericEpithet("InfraGeneric");
 825                 botName.setSpecificEpithet("specificEpithet");
 826                 botName.setInfraSpecificEpithet("infraSpecificEpithet");
 827                 Person combinationAuthorship = Person.NewInstance();
 828                 botName.setCombinationAuthorship(combinationAuthorship);
 829                 Person exCombinationAuthorship = Person.NewInstance();
 830                 botName.setExCombinationAuthorship(exCombinationAuthorship);
 831                 Person basionymAuthorship = Person.NewInstance();
 832                 botName.setBasionymAuthorship(basionymAuthorship);
 833                 Person exBasionymAuthorship = Person.NewInstance();
 834                 botName.setExBasionymAuthorship(exBasionymAuthorship);
 835                 handleIdentifiableEntity(botName);
 836                 handleAnnotatableEntity(botName.getHomotypicalGroup());
 837                 BotanicalName botName2 = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
 838                 HybridRelationship hybridRel = botName2.addHybridChild(botName, HybridRelationshipType.FIRST_PARENT(), "Rule 1.2.3");
 839                 hybridRel.setCitation(ReferenceFactory.newBook());
 840                 hybridRel.setCitationMicroReference("p. 123");
 841                 handleAnnotatableEntity(hybridRel);
 842
 843                 ZoologicalName zooName = TaxonNameFactory.NewZoologicalInstance(Rank.GENUS());
 844                 zooName.setBreed("breed");
 845                 zooName.setPublicationYear(1922);
 846                 zooName.setOriginalPublicationYear(1987);
 847                 zooName.setAppendedPhrase("appended phrase");
 848                 zooName.addDescription(TaxonNameDescription.NewInstance());
 849                 zooName.setNomenclaturalMicroReference("p. 123");
 850                 zooName.setNomenclaturalReference(getReference());
 851                 NameRelationship rel = zooName.addRelationshipFromName(botName, NameRelationshipType.LATER_HOMONYM() , "ruleConsidered");
 852                 NomenclaturalStatus status = NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED(), getReference(), "p. 222");
 853                 zooName.addStatus(status);
 854                 handleAnnotatableEntity(rel);
 855                 handleAnnotatableEntity(status);
 856                 handleIdentifiableEntity(zooName);
 857
 858                 //TypeDesignation
 859                 ZoologicalName speciesZooName = TaxonNameFactory.NewZoologicalInstance(Rank.SPECIES());
 860                 NameTypeDesignation nameDesig = zooName.addNameTypeDesignation(speciesZooName, getReference(), "111", "original name",
 861                                 NameTypeDesignationStatus.AUTOMATIC(), true, true, true, true);
 862                 handleAnnotatableEntity(nameDesig);
 863                 SpecimenTypeDesignation specimenDesig = speciesZooName.addSpecimenTypeDesignation(getSpecimen(), SpecimenTypeDesignationStatus.HOLOTYPE(),
 864                                 getReference(), "p,22", "original name", false, true);
 865                 handleAnnotatableEntity(specimenDesig);
 866
 867                 ViralName viralName = TaxonNameFactory.NewViralInstance(Rank.GENUS());
 868                 viralName.setAcronym("acronym");
 869                 handleIdentifiableEntity(viralName);
 870
 871
 872                 cdmBases.add(bacName);
 873                 cdmBases.add(botName);
 874                 cdmBases.add(viralName);
 875                 cdmBases.add(zooName);
 876         }
 877
 878         private void handleEventBase(EventBase event){
 879                 event.setTimeperiod(TimePeriodParser.parseString("1.4.1975-2.5.1980"));
 880                 event.setActor(Person.NewTitledInstance("EventActor"));
 881                 event.setDescription("Some interesing event");
 882         }
 883
 884         private void handleAnnotatableEntity(AnnotatableEntity entity){
 885                 Annotation annotation = Annotation.NewDefaultLanguageInstance("annotation");
 886                 entity.addAnnotation(annotation);
 887                 Marker marker = Marker.NewInstance(MarkerType.COMPLETE(), true);
 888                 entity.addMarker(marker);
 889         }
 890
 891         private void handleIdentifiableEntity(IdentifiableEntity<?> identifiableEntity){
 892                 handleAnnotatableEntity(identifiableEntity);
 893
 894                 //Credits
 895                 Person creditor = Person.NewTitledInstance("Creditor");
 896                 Credit credit = Credit.NewInstance(creditor, "credit");
 897                 identifiableEntity.addCredit(credit);
 898
 899                 //Extension
 900                 Extension.NewInstance(identifiableEntity, "extension", ExtensionType.INFORMAL_CATEGORY());
 901
 902                 //Identifier
 903                 Identifier<?> identifier = identifiableEntity.addIdentifier("ident23", DefinedTerm.SEX_FEMALE());
 904                 handleAnnotatableEntity(identifier);
 905
 906
 907                 //Rights
 908                 Rights rights = Rights.NewInstance("right", Language.ENGLISH());
 909                 rights.setUri(URI.create("http://rights.abc.de"));
 910                 rights.setAbbreviatedText("abbrev");
 911                 rights.setType(RightsType.COPYRIGHT());
 912                 Person owner = Person.NewTitledInstance("Owner");
 913                 rights.setAgent(owner);
 914                 identifiableEntity.addRights(rights);
 915
 916                 if (identifiableEntity.isInstanceOf(IdentifiableMediaEntity.class)){
 917                         Media media = Media.NewInstance(URI.create("http://www.identifiableMedia.de"), 22, "img/jpg", "jpg");
 918                         ((IdentifiableMediaEntity<?>)identifiableEntity).addMedia(media);
 919                 }
 920
 921                 //source
 922                 IdentifiableSource source = identifiableEntity.addSource(OriginalSourceType.Import, "id", "idNamespace",
 923                                 getReference(), "123");
 924                 source.setOriginalNameString("original name");
 925
 926                 //LSID
 927                  try {
 928                         LSID lsid = new LSID("urn:lsid:a.b.de:namespace:1234");
 929                         identifiableEntity.setLsid(lsid);
 930                 } catch (MalformedLSIDException e) {
 931                         e.printStackTrace();
 932                 }
 933
 934
 935         }
 936
 937
 938         private Reference getReference() {
 939                  Reference result = ReferenceFactory.newGeneric();
 940                  result.setTitle("some generic reference");
 941                  return result;
 942         }
 943
 944
 945         private DerivedUnit getSpecimen() {
 946                 DerivedUnit derivedUnit = DerivedUnit.NewPreservedSpecimenInstance();
 947                 return derivedUnit;
 948         }
 949
 950
 951
 952         private Taxon getTaxon() {
 953                 Reference sec = getReference();
 954                 TaxonNameBase<?,?> name = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
 955                 Taxon taxon = Taxon.NewInstance(name, sec);
 956                 return taxon;
 957
 958         }
 959 }