cdmlib-persistence/src/test/java/eu/etaxonomy/cdm/datagenerator/FullCoverageDataGenerator.java

   1 /**
   2  *
   3  */
   4 package eu.etaxonomy.cdm.datagenerator;
   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.Extension;
  27 import eu.etaxonomy.cdm.model.common.ExtensionType;
  28 import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
  29 import eu.etaxonomy.cdm.model.common.IdentifiableSource;
  30 import eu.etaxonomy.cdm.model.common.LSID;
  31 import eu.etaxonomy.cdm.model.common.Language;
  32 import eu.etaxonomy.cdm.model.common.Marker;
  33 import eu.etaxonomy.cdm.model.common.MarkerType;
  34 import eu.etaxonomy.cdm.model.common.OriginalSourceType;
  35 import eu.etaxonomy.cdm.model.common.Representation;
  36 import eu.etaxonomy.cdm.model.common.TermType;
  37 import eu.etaxonomy.cdm.model.description.CategoricalData;
  38 import eu.etaxonomy.cdm.model.description.CommonTaxonName;
  39 import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
  40 import eu.etaxonomy.cdm.model.description.Distribution;
  41 import eu.etaxonomy.cdm.model.description.Feature;
  42 import eu.etaxonomy.cdm.model.description.FeatureNode;
  43 import eu.etaxonomy.cdm.model.description.FeatureTree;
  44 import eu.etaxonomy.cdm.model.description.IIdentificationKey;
  45 import eu.etaxonomy.cdm.model.description.IndividualsAssociation;
  46 import eu.etaxonomy.cdm.model.description.MeasurementUnit;
  47 import eu.etaxonomy.cdm.model.description.MediaKey;
  48 import eu.etaxonomy.cdm.model.description.MultiAccessKey;
  49 import eu.etaxonomy.cdm.model.description.PolytomousKey;
  50 import eu.etaxonomy.cdm.model.description.PolytomousKeyNode;
  51 import eu.etaxonomy.cdm.model.description.PresenceTerm;
  52 import eu.etaxonomy.cdm.model.description.QuantitativeData;
  53 import eu.etaxonomy.cdm.model.description.SpecimenDescription;
  54 import eu.etaxonomy.cdm.model.description.State;
  55 import eu.etaxonomy.cdm.model.description.StateData;
  56 import eu.etaxonomy.cdm.model.description.TaxonDescription;
  57 import eu.etaxonomy.cdm.model.description.TaxonInteraction;
  58 import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
  59 import eu.etaxonomy.cdm.model.description.TextData;
  60 import eu.etaxonomy.cdm.model.description.TextFormat;
  61 import eu.etaxonomy.cdm.model.description.WorkingSet;
  62 import eu.etaxonomy.cdm.model.location.Country;
  63 import eu.etaxonomy.cdm.model.location.NamedArea;
  64 import eu.etaxonomy.cdm.model.location.Point;
  65 import eu.etaxonomy.cdm.model.location.ReferenceSystem;
  66 import eu.etaxonomy.cdm.model.media.AudioFile;
  67 import eu.etaxonomy.cdm.model.media.ImageFile;
  68 import eu.etaxonomy.cdm.model.media.Media;
  69 import eu.etaxonomy.cdm.model.media.MediaRepresentation;
  70 import eu.etaxonomy.cdm.model.media.MovieFile;
  71 import eu.etaxonomy.cdm.model.media.Rights;
  72 import eu.etaxonomy.cdm.model.media.RightsType;
  73 import eu.etaxonomy.cdm.model.molecular.Amplification;
  74 import eu.etaxonomy.cdm.model.molecular.Cloning;
  75 import eu.etaxonomy.cdm.model.molecular.DnaSample;
  76 import eu.etaxonomy.cdm.model.molecular.PhylogeneticTree;
  77 import eu.etaxonomy.cdm.model.molecular.Primer;
  78 import eu.etaxonomy.cdm.model.molecular.Sequence;
  79 import eu.etaxonomy.cdm.model.molecular.SequenceDirection;
  80 import eu.etaxonomy.cdm.model.molecular.SequenceString;
  81 import eu.etaxonomy.cdm.model.molecular.SingleRead;
  82 import eu.etaxonomy.cdm.model.name.BacterialName;
  83 import eu.etaxonomy.cdm.model.name.BotanicalName;
  84 import eu.etaxonomy.cdm.model.name.CultivarPlantName;
  85 import eu.etaxonomy.cdm.model.name.NameRelationshipType;
  86 import eu.etaxonomy.cdm.model.name.NameTypeDesignationStatus;
  87 import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;
  88 import eu.etaxonomy.cdm.model.name.NomenclaturalStatusType;
  89 import eu.etaxonomy.cdm.model.name.Rank;
  90 import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignationStatus;
  91 import eu.etaxonomy.cdm.model.name.TaxonNameBase;
  92 import eu.etaxonomy.cdm.model.name.ViralName;
  93 import eu.etaxonomy.cdm.model.name.ZoologicalName;
  94 import eu.etaxonomy.cdm.model.occurrence.Collection;
  95 import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
  96 import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
  97 import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
  98 import eu.etaxonomy.cdm.model.occurrence.DeterminationEvent;
  99 import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
 100 import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
 101 import eu.etaxonomy.cdm.model.occurrence.MaterialOrMethodEvent;
 102 import eu.etaxonomy.cdm.model.occurrence.MediaSpecimen;
 103 import eu.etaxonomy.cdm.model.occurrence.PreservationMethod;
 104 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
 105 import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
 106 import eu.etaxonomy.cdm.model.reference.Reference;
 107 import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
 108 import eu.etaxonomy.cdm.model.taxon.Classification;
 109 import eu.etaxonomy.cdm.model.taxon.Synonym;
 110 import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
 111 import eu.etaxonomy.cdm.model.taxon.Taxon;
 112 import eu.etaxonomy.cdm.model.taxon.TaxonNode;
 113 import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
 114 import eu.etaxonomy.cdm.strategy.parser.TimePeriodParser;
 115
 116 /**
 117  * This class tries to create a database that has
 118  * at least one record in each database.
 119  * It is meant to test update scripts as well as imports
 120  * and exports.
 121  * ATTENTION: As the content of the created database may change
 122  * over time due to model changes and other requirements test using
 123  * this class should be written in a way that they do rather
 124  * depend on general parameter than concrete data values.
 125  *
 126  * @author a.mueller
 127  * @created 3013-12-02
 128  *
 129  * TODO under construction
 130  *
 131  */
 132 public class FullCoverageDataGenerator {
 133
 134
 135         public void fillWithData(Session session){
 136                 List<CdmBase> cdmBases = new ArrayList<CdmBase>();
 137
 138                 createAgents(cdmBases);
 139
 140                 createDescriptions(cdmBases);
 141
 142                 createMedia(cdmBases);
 143
 144                 createMolecular(cdmBases);
 145
 146                 createTaxonName(cdmBases);
 147
 148                 createOccurrence(cdmBases);
 149
 150                 createReference(cdmBases);
 151
 152                 createTaxon(cdmBases);
 153
 154                 for (CdmBase cdmBase: cdmBases){
 155                         session.save(cdmBase);
 156                 }
 157         }
 158
 159
 160         /**
 161          * @param cdmBases
 162          */
 163         private void createAgents(List<CdmBase> cdmBases) {
 164                 //Person
 165                 Person person = Person.NewTitledInstance("Person Title");
 166                 person.setFirstname("first name");
 167                 person.setLastname("last name");
 168                 person.setLifespan(TimePeriodParser.parseString("1905-1995"));
 169                 person.setPrefix("prefix");
 170                 person.setSuffix("suffix");
 171
 172                 handleIdentifiableEntity(person);
 173
 174                 //Contact
 175                 Contact contact = Contact.NewInstance();
 176                 person.setContact(contact);
 177                 Point locality = Point.NewInstance(45.12, -38.69, ReferenceSystem.WGS84(), 22);
 178                 contact.addEmailAddress("a@b.de");
 179                 contact.addFaxNumber("f:010-123456");
 180                 contact.addPhoneNumber("p:090-987654");
 181                 contact.addUrl(URI.create("http://www.abc.de").toString());
 182
 183                 //Address
 184                 Address address = Address.NewInstance(Country.GERMANY(), "locality", "pobox", "12345", "region", "street", locality);
 185                 contact.addAddress(address);
 186
 187                 //Team
 188                 Team team = Team.NewTitledInstance("Team title", "Team abbrev title");
 189                 team.addTeamMember(person);
 190
 191                 //Institution
 192                 Institution institution = Institution.NewInstance();
 193                 institution.setCode("institution code");
 194                 institution.setName("institution name");
 195
 196                 //TODO vocabulary
 197 //              voc = "29ad808b-3126-4274-be81-4561e7afc76f"
 198                 DefinedTerm instType = DefinedTerm.NewInstitutionTypeInstance("Description forthis instition type", "institution type", "inst. t.");
 199                 institution.addType(instType);
 200                 person.addInstitutionalMembership(institution, TimePeriodParser.parseString("1955-1956"), "department", "role");
 201
 202                 Institution subInstitution = Institution.NewInstance();
 203                 subInstitution.setCode("sub institution code");
 204                 subInstitution.setName("sub institution name");
 205                 subInstitution.setIsPartOf(institution);
 206
 207                 cdmBases.add(person);
 208                 cdmBases.add(team);
 209         }
 210
 211
 212         private void createDescriptions(List<CdmBase> cdmBases) {
 213
 214                 //Categorical data
 215                 State state = State.NewInstance("Test state", "state", "st.");
 216                 CategoricalData categoricalData = CategoricalData.NewInstance(state, Feature.CONSERVATION());
 217                 StateData stateData = categoricalData.getStateData().get(0);
 218                 stateData.addModifier(DefinedTerm.SEX_FEMALE());
 219
 220                 StateData stateData2 = StateData.NewInstance(State.NewInstance());
 221                 stateData2.putModifyingText(Language.ENGLISH(), "State2 modifying text");
 222                 categoricalData.addStateData(stateData2);
 223
 224
 225                 categoricalData.setOrderRelevant(true);
 226
 227                 //Quantitative data
 228                 Feature leaveLength = Feature.NewInstance("Leave length description", "leave length", "l.l.");
 229                 leaveLength.setSupportsQuantitativeData(true);
 230                 QuantitativeData quantitativeData = QuantitativeData.NewInstance(leaveLength);
 231                 MeasurementUnit measurementUnit = MeasurementUnit.NewInstance("Measurement Unit", "munit", null);
 232                 quantitativeData.setUnit(measurementUnit);
 233                 quantitativeData.setAverage((float)22.9 , null);
 234
 235
 236                 CommonTaxonName commonTaxonName = CommonTaxonName.NewInstance("common name", Language.ENGLISH(), Country.UNITEDSTATESOFAMERICA());
 237
 238                 TextData textData = TextData.NewInstance(Feature.DIAGNOSIS());
 239                 textData.putModifyingText(Language.ENGLISH(), "nice diagnosis");
 240
 241                 TextFormat format = TextFormat.NewInstance("format", "format", null);
 242                 textData.setFormat(format);
 243
 244                 DerivedUnit specimen = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
 245                 IndividualsAssociation indAssoc = IndividualsAssociation.NewInstance(specimen);
 246                 indAssoc.putDescription(Language.ENGLISH(), "description for individuals association");
 247
 248                 TaxonInteraction taxonInteraction = TaxonInteraction.NewInstance(Feature.HOSTPLANT());
 249                 taxonInteraction.putDescription(Language.ENGLISH(), "interaction description");
 250
 251
 252                 Distribution distribution = Distribution.NewInstance(Country.GERMANY(), PresenceTerm.CULTIVATED());
 253
 254
 255                 Taxon taxon = getTaxon();
 256                 TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon);
 257                 taxonDescription.addElements(categoricalData, quantitativeData,
 258                                 textData, commonTaxonName, taxonInteraction, indAssoc, distribution);
 259
 260                 DerivedUnit describedSpecimenOrObservation = DerivedUnit.NewInstance(SpecimenOrObservationType.DerivedUnit);
 261                 taxonDescription.setDescribedSpecimenOrObservation(describedSpecimenOrObservation);
 262
 263                 taxonDescription.addScope(DefinedTerm.SEX_FEMALE());
 264                 taxonDescription.addGeoScope(Country.GERMANY());
 265
 266                 cdmBases.add(taxon);
 267
 268                 //DescriptionElmenetBase  + source
 269                 textData.addMedia(Media.NewInstance());
 270                 textData.addModifier(DefinedTerm.SEX_HERMAPHRODITE());
 271                 textData.putModifyingText(Language.ENGLISH(), "no modification");
 272                 textData.setTimeperiod(TimePeriodParser.parseString("1970-1980"));
 273                 Reference<?> ref = ReferenceFactory.newArticle();
 274                 DescriptionElementSource source = textData.addSource(OriginalSourceType.Import, "22", "taxon description table", ref, "detail");
 275                 source.setNameUsedInSource(BotanicalName.NewInstance(Rank.GENUS()));
 276
 277
 278
 279                 //Specimen description
 280                 SpecimenOrObservationBase<?> describedSpecimen = getSpecimen();
 281                 SpecimenDescription.NewInstance(specimen);
 282                 cdmBases.add(describedSpecimen);
 283
 284                 //Name description
 285                 TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
 286                 TaxonNameDescription.NewInstance(name);
 287                 cdmBases.add(name);
 288
 289                 //Feature Tree
 290                 FeatureTree featureTree = FeatureTree.NewInstance();
 291                 FeatureNode descriptionFeatureNode = FeatureNode.NewInstance(Feature.DESCRIPTION());
 292                 FeatureNode leaveLengthNode = FeatureNode.NewInstance(leaveLength);
 293                 featureTree.getRootChildren().add(descriptionFeatureNode);
 294                 descriptionFeatureNode.addChild(leaveLengthNode);
 295
 296                 State inapplicableState = State.NewInstance("inapplicableState", "inapplicableState", null);
 297                 State applicableState = State.NewInstance("only applicable state", "only applicable state", null);
 298                 leaveLengthNode.addInapplicableState(inapplicableState);
 299                 leaveLengthNode.addApplicableState(applicableState);
 300                 cdmBases.add(featureTree);
 301
 302
 303                 WorkingSet workingSet = WorkingSet.NewInstance();
 304                 workingSet.addDescription(taxonDescription);
 305                 workingSet.setLabel("My Workingset");
 306                 workingSet.getDescriptiveSystem();
 307
 308
 309                 //polytomous keys
 310                 Taxon coveredTaxon = Taxon.NewInstance(name, null);
 311                 PolytomousKey key = PolytomousKey.NewTitledInstance("My Polykey");
 312                 handleIdentificationKey(key, taxon, coveredTaxon);
 313                 key.setStartNumber(10);
 314
 315
 316                 PolytomousKeyNode firstChildNode = PolytomousKeyNode.NewInstance("Green", "What is the leave length?", coveredTaxon, leaveLength);
 317                 key.getRoot().addChild(firstChildNode);
 318                 PolytomousKeyNode secondChildNode = PolytomousKeyNode.NewInstance("234");
 319                 firstChildNode.addChild(secondChildNode);
 320
 321                 PolytomousKey subkey = PolytomousKey.NewTitledInstance("Sub-key");
 322                 firstChildNode.setSubkey(subkey);
 323
 324                 PolytomousKeyNode subKeyNode = PolytomousKeyNode.NewInstance("sub key couplet");
 325                 subkey.getRoot().addChild(subKeyNode);
 326                 secondChildNode.setOtherNode(subKeyNode);
 327
 328                 secondChildNode.putModifyingText(Language.GERMAN(), "manchmal");
 329
 330                 cdmBases.add(key);
 331                 cdmBases.add(subkey);
 332
 333                 MediaKey mediaKey = MediaKey.NewInstance();
 334                 mediaKey.addKeyRepresentation(Representation.NewInstance("Media Key Representation", "media key", null, Language.ENGLISH()));
 335                 handleIdentificationKey(mediaKey, taxon, coveredTaxon);
 336
 337                 MultiAccessKey multiAccessKey = MultiAccessKey.NewInstance();
 338                 handleIdentificationKey(multiAccessKey, taxon, coveredTaxon);
 339
 340                 cdmBases.add(mediaKey);
 341                 cdmBases.add(multiAccessKey);
 342
 343         }
 344
 345
 346
 347         private void handleIdentificationKey(IIdentificationKey key, Taxon taxon, Taxon coveredTaxon){
 348                 key.addCoveredTaxon(coveredTaxon);
 349                 key.addGeographicalScope(Country.GERMANY());
 350                 key.addScopeRestriction(DefinedTerm.SEX_FEMALE());
 351                 key.addTaxonomicScope(taxon);
 352         }
 353
 354
 355         private void createMedia(List<CdmBase> cdmBases){
 356                 AudioFile audioFile = AudioFile.NewInstance(URI.create("http://a.b.de"), 22);
 357                 ImageFile imageFile = ImageFile.NewInstance(URI.create("http://b.c.de"), 44, 467, 55);
 358                 MovieFile movieFile = MovieFile.NewInstance(URI.create("http://b.c.de"), 67);
 359                 MediaRepresentation mediaRepresentation = MediaRepresentation.NewInstance("mime", "media");
 360
 361                 mediaRepresentation.addRepresentationPart(movieFile);
 362                 mediaRepresentation.addRepresentationPart(imageFile);
 363                 mediaRepresentation.addRepresentationPart(audioFile);
 364                 Media media = Media.NewInstance();
 365                 media.addRepresentation(mediaRepresentation);
 366
 367                 media.putTitle(Language.ENGLISH(), "Media title");
 368                 media.setMediaCreated(DateTime.now());
 369                 media.putDescription(Language.ENGLISH(), "Media description");
 370
 371                 Person artist = Person.NewTitledInstance("artist");
 372                 media.setArtist(artist);
 373                 cdmBases.add(media);
 374                 cdmBases.add(artist);
 375         }
 376
 377
 378         private void createMolecular(List<CdmBase> cdmBases) {
 379                 DnaSample dnaSample = DnaSample.NewInstance();
 380
 381                 //Amplification
 382                 Amplification amplification = Amplification.NewInstance(dnaSample);
 383                 DefinedTerm dnaMarker = DefinedTerm.NewDnaMarkerInstance("My dna marker", "dna marker", null);
 384                 amplification.setDnaMarker(dnaMarker);
 385                 amplification.setSuccessful(true);
 386                 amplification.setSuccessText("Very successful");
 387
 388                 Primer forwardPrimer = Primer.NewInstance("forward primer");
 389                 forwardPrimer.setPublishedIn(getReference());
 390                 forwardPrimer.setSequence(Sequence.NewInstance("my sequence"));
 391
 392                 Primer reversePrimer = Primer.NewInstance("reverse primer");
 393
 394                 amplification.setForwardPrimer(forwardPrimer);
 395                 amplification.setReversePrimer(reversePrimer);
 396
 397                 DefinedTerm cloningMethod = DefinedTerm.NewInstance(TermType.MaterialOrMethod, "cloning method", "cloning method", null);
 398                 Cloning cloning = Cloning.NewInstance(cloningMethod, "My cloning method", "my strain", forwardPrimer, reversePrimer);
 399                 amplification.setCloning(cloning);
 400
 401                 DefinedTerm purificationMethod = DefinedTerm.NewInstance(TermType.MaterialOrMethod, "purification method", "purification method", null);
 402                 MaterialOrMethodEvent purification = MaterialOrMethodEvent.NewInstance(purificationMethod, "purification method");
 403                 amplification.setPurification(purification);
 404
 405
 406                 amplification.setLadderUsed("ladder");
 407                 amplification.setElectrophoresisVoltage(5.5);
 408                 amplification.setGelConcentration(2.4);
 409                 amplification.setGelRunningTime(3.6);
 410                 Media gelPhoto = Media.NewInstance();
 411                 amplification.setGelPhoto(gelPhoto);
 412
 413                 //SingleRead
 414                 SingleRead singleRead = SingleRead.NewInstance();
 415                 amplification.addSingleRead(singleRead);
 416                 MaterialOrMethodEvent readEvent = MaterialOrMethodEvent.NewInstance(null, "read method");
 417
 418                 singleRead.setMaterialOrMethod(readEvent);
 419                 Media pherogram = Media.NewInstance();
 420                 singleRead.setPherogram(pherogram);
 421
 422                 singleRead.setPrimer(forwardPrimer);
 423                 singleRead.setSequence(SequenceString.NewInstance("ABTC"));
 424                 singleRead.setDirection(SequenceDirection.Forward);
 425
 426                 //Seuqence
 427                 Sequence sequence = Sequence.NewInstance("ADDT");
 428                 dnaSample.addSequence(sequence);
 429                 sequence.addSingleRead(singleRead);
 430                 Media contigFile = Media.NewInstance();
 431                 sequence.setContigFile(contigFile);
 432                 sequence.setIsBarcode(true);
 433                 sequence.setDnaMarker(dnaMarker);
 434                 sequence.setBarcodeSequencePart(SequenceString.NewInstance("ADTA"));
 435                 sequence.setGeneticAccessionNumber("GenNO12345");
 436                 sequence.setBoldProcessId("boldId");
 437                 sequence.setHaplotype("haplotype");
 438                 Reference<?> sequenceCitation = getReference();
 439                 sequence.addCitation(sequenceCitation);
 440
 441
 442                 //Phylogenetic Tree
 443                 PhylogeneticTree phyloTree = PhylogeneticTree.NewInstance();
 444                 phyloTree.addUsedSequences(sequence);
 445
 446                 cdmBases.add(dnaSample);
 447                 cdmBases.add(phyloTree);
 448         }
 449
 450
 451         private void createTaxon(List<CdmBase> cdmBases) {
 452                 Reference<?> sec = getReference();
 453                 TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
 454                 Taxon taxon = Taxon.NewInstance(name, sec);
 455
 456                 TaxonNameBase<?,?> synName = BotanicalName.NewInstance(Rank.GENUS());
 457                 Synonym syn = Synonym.NewInstance(synName, sec);
 458                 taxon.addSynonym(syn, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(),
 459                                 getReference(), "123");
 460                 taxon.setDoubtful(true);
 461
 462                 Taxon concept = Taxon.NewInstance(name, getReference());
 463                 taxon.addTaxonRelation(concept, TaxonRelationshipType.CONGRUENT_TO(),
 464                                 sec, "444");
 465                 taxon.setTaxonStatusUnknown(true);
 466                 taxon.setUnplaced(true);
 467                 taxon.setExcluded(true);
 468
 469                 //Classification
 470                 Classification classification = Classification.NewInstance("My classification", sec);
 471                 TaxonNode node = classification.addChildTaxon(taxon, sec,"22");
 472
 473                 Taxon childTaxon = Taxon.NewInstance(synName, sec);
 474                 node.addChildTaxon(childTaxon, sec, "44");
 475
 476                 cdmBases.add(taxon);
 477                 cdmBases.add(concept);
 478                 cdmBases.add(childTaxon);
 479                 cdmBases.add(classification);
 480
 481
 482         }
 483
 484
 485
 486
 487         private void createReference(List<CdmBase> cdmBases) {
 488                 Reference<?> reference = ReferenceFactory.newArticle();
 489                 Person author = Person.NewTitledInstance("Author team");
 490                 reference.setAuthorTeam(author);
 491                 reference.setTitle("ref title");
 492                 reference.setAbbrevTitle("abbrev title");
 493                 reference.setDatePublished(TimePeriodParser.parseString("1999"));
 494                 reference.setEdition("edition");
 495                 reference.setEditor("editor");
 496                 Institution institution = Institution.NewInstance();
 497                 reference.setInstitution(institution);
 498                 reference.setIsbn("1234556");
 499                 reference.setIssn("issn");
 500                 reference.setDoi(DOI.fromRegistrantCodeAndSuffix("14356", "suffix"));
 501                 reference.setReferenceAbstract("referenceAbstract");
 502                 reference.setOrganization("organization");
 503                 reference.setPages("123-134");
 504                 reference.setPlacePublished("place Published");
 505                 reference.setPublisher("publisher");
 506                 Institution school = Institution.NewInstance();
 507                 reference.setSchool(school);
 508 //              reference.setSeriesPart("series");
 509                 reference.setSeriesPart("seriesPart");
 510                 reference.setVolume("vol. 3");
 511                 reference.setUri(URI.create("http://rer.abc.de"));
 512
 513                 Reference<?> journal = ReferenceFactory.newJournal();
 514                 reference.setInJournal(journal);
 515
 516                 cdmBases.add(reference);
 517
 518         }
 519
 520
 521
 522
 523         private void createOccurrence(List<CdmBase> cdmBases) {
 524                 //Collection
 525                 Collection collection = Collection.NewInstance();
 526                 Collection subCollection = Collection.NewInstance();
 527                 subCollection.setSuperCollection(collection);
 528
 529                 collection.setCode("coll code");
 530                 collection.setCodeStandard("codeStandard");
 531                 collection.setName("coll name");
 532                 collection.setTownOrLocation("townOrLocation");
 533                 Institution institution = Institution.NewInstance();
 534                 collection.setInstitute(institution);
 535
 536                 //FieldUnit
 537                 FieldUnit fieldUnit = FieldUnit.NewInstance();
 538                 fieldUnit.setFieldNumber("fieldNumber");
 539                 fieldUnit.setFieldNotes("fieldNotes");
 540                 Person primaryCollector = Person.NewInstance();
 541                 fieldUnit.setPrimaryCollector(primaryCollector);
 542
 543                 GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
 544                 fieldUnit.setGatheringEvent(gatheringEvent);
 545                 gatheringEvent.putLocality(Language.ENGLISH(), "locality");
 546                 gatheringEvent.setExactLocation(Point.NewInstance(22.4, -34.2,
 547                                 ReferenceSystem.WGS84(), 33));
 548                 gatheringEvent.setCountry(Country.GERMANY());
 549                 gatheringEvent.addCollectingArea(NamedArea.EUROPE());
 550                 gatheringEvent.setCollectingMethod("collectingMethod");
 551                 gatheringEvent.setAbsoluteElevation(10);
 552                 gatheringEvent.setAbsoluteElevationMax(100);
 553                 gatheringEvent.setAbsoluteElevationText("elevation text");
 554
 555                 gatheringEvent.setDistanceToGround(10.4);
 556                 gatheringEvent.setDistanceToGroundMax(100.3);
 557                 gatheringEvent.setDistanceToGroundText("distance to ground text");
 558
 559                 gatheringEvent.setDistanceToWaterSurface(10.4);
 560                 gatheringEvent.setDistanceToWaterSurfaceMax(100.3);
 561                 gatheringEvent.setDistanceToWaterSurfaceText("distance to water text");
 562
 563
 564                 //Derived Unit
 565                 MediaSpecimen mediaSpecimen = MediaSpecimen.NewInstance(SpecimenOrObservationType.StillImage);
 566                 mediaSpecimen.setCollection(collection);
 567                 mediaSpecimen.setCatalogNumber("catalogNumber");
 568                 mediaSpecimen.setAccessionNumber("accessionNumber");
 569 //              mediaSpecimen.setCollectorsNumber("collectorsNumber");
 570                 mediaSpecimen.setBarcode("barcode");
 571                 BotanicalName storedUnder = BotanicalName.NewInstance(Rank.SPECIES());
 572                 storedUnder.setTitleCache("Stored under", true);
 573                 mediaSpecimen.setStoredUnder(storedUnder);
 574                 mediaSpecimen.setExsiccatum("exsiccatum");
 575                 PreservationMethod preservation = PreservationMethod.NewInstance(null, "My preservation");
 576                 preservation.setTemperature(22.4);
 577                 mediaSpecimen.setPreservation(preservation);
 578
 579                 //DerivationEvent
 580                 DerivationEvent event = DerivationEvent.NewInstance(DerivationEventType.ACCESSIONING());
 581                 event.addOriginal(fieldUnit);
 582                 event.addDerivative(mediaSpecimen);
 583
 584
 585                 //SpecOrObservationBase
 586                 fieldUnit.setSex(DefinedTerm.SEX_FEMALE());
 587                 fieldUnit.setLifeStage(DefinedTerm.NewStageInstance("Live stage", "stage", null));
 588                 fieldUnit.setKindOfUnit(DefinedTerm.NewKindOfUnitInstance("Kind of unit", "Kind of unit", null));
 589                 fieldUnit.setIndividualCount(3);
 590                 fieldUnit.putDefinition(Language.ENGLISH(), "definition");
 591                 fieldUnit.setPublish(true);
 592
 593                 //Determination
 594                 DeterminationEvent determinationEvent = DeterminationEvent.NewInstance(getTaxon(), mediaSpecimen);
 595                 determinationEvent.setModifier(DefinedTerm.DETERMINATION_MODIFIER_AFFINIS());
 596                 determinationEvent.setPreferredFlag(true);
 597                 determinationEvent.addReference(getReference());
 598
 599                 cdmBases.add(fieldUnit);
 600                 cdmBases.add(mediaSpecimen);
 601                 cdmBases.add(collection);
 602         }
 603
 604
 605         private void createTaxonName(List<CdmBase> cdmBases) {
 606                 BacterialName bacName = BacterialName.NewInstance(Rank.GENUS());
 607                 bacName.setSubGenusAuthorship("sub Genus author");
 608                 bacName.setNameApprobation("nameApprobation");
 609
 610                 CultivarPlantName botName = CultivarPlantName.NewInstance(Rank.SUBSPECIES());
 611                 botName.setAnamorphic(true);
 612                 botName.setCultivarName("cultivarName");
 613                 botName.setGenusOrUninomial("Genus");
 614                 botName.setInfraGenericEpithet("InfraGeneric");
 615                 botName.setSpecificEpithet("specificEpithet");
 616                 botName.setInfraSpecificEpithet("infraSpecificEpithet");
 617                 Person combinationAuthorTeam = Person.NewInstance();
 618                 botName.setCombinationAuthorTeam(combinationAuthorTeam);
 619                 Person exCombinationAuthorTeam = Person.NewInstance();
 620                 botName.setExCombinationAuthorTeam(exCombinationAuthorTeam);
 621                 Person basionymAuthorTeam = Person.NewInstance();
 622                 botName.setBasionymAuthorTeam(basionymAuthorTeam);
 623                 Person exBasionymAuthorTeam = Person.NewInstance();
 624                 botName.setExBasionymAuthorTeam(exBasionymAuthorTeam);
 625
 626                 ZoologicalName zooName = ZoologicalName.NewInstance(Rank.GENUS());
 627                 zooName.setBreed("breed");
 628                 zooName.setPublicationYear(1922);
 629                 zooName.setOriginalPublicationYear(1987);
 630                 zooName.setAppendedPhrase("appended phrase");
 631                 zooName.addDescription(TaxonNameDescription.NewInstance());
 632                 zooName.setNomenclaturalMicroReference("p. 123");
 633                 zooName.setNomenclaturalReference(getReference());
 634                 zooName.addRelationshipFromName(botName, NameRelationshipType.LATER_HOMONYM() , "ruleConsidered");
 635                 zooName.addStatus(NomenclaturalStatus.NewInstance(NomenclaturalStatusType.CONSERVED(), getReference(), "p. 222"));
 636
 637                 //TypeDesignation
 638                 ZoologicalName speciesZooName = ZoologicalName.NewInstance(Rank.SPECIES());
 639                 zooName.addNameTypeDesignation(speciesZooName, getReference(), "111", "original name",
 640                                 NameTypeDesignationStatus.AUTOMATIC(), true, true, true, true);
 641                 speciesZooName.addSpecimenTypeDesignation(getSpecimen(), SpecimenTypeDesignationStatus.HOLOTYPE(),
 642                                 getReference(), "p,22", "original name", false, true);
 643
 644
 645                 ViralName viralName = ViralName.NewInstance(Rank.GENUS());
 646                 viralName.setAcronym("acronym");
 647
 648                 cdmBases.add(bacName);
 649                 cdmBases.add(botName);
 650                 cdmBases.add(viralName);
 651                 cdmBases.add(zooName);
 652         }
 653
 654         private void handleAnnotatableEntity(AnnotatableEntity entity){
 655                 Annotation annotation = Annotation.NewDefaultLanguageInstance("annotation");
 656                 entity.addAnnotation(annotation);
 657                 Marker marker = Marker.NewInstance(MarkerType.COMPLETE(), true);
 658                 entity.addMarker(marker);
 659         }
 660
 661         private void handleIdentifiableEntity(IdentifiableEntity<?> identifiableEntity){
 662                 handleAnnotatableEntity(identifiableEntity);
 663
 664                 //Credits
 665                 Person creditor = Person.NewTitledInstance("Creditor");
 666                 Credit credit = Credit.NewInstance(creditor, "credit");
 667                 identifiableEntity.addCredit(credit);
 668
 669                 //Extension
 670                 Extension.NewInstance(identifiableEntity, "extension", ExtensionType.INFORMAL_CATEGORY());
 671
 672                 //Rights
 673                 Rights rights = Rights.NewInstance("right", Language.ENGLISH());
 674                 rights.setUri(URI.create("http://rights.abc.de"));
 675                 rights.setAbbreviatedText("abbrev");
 676                 rights.setType(RightsType.COPYRIGHT());
 677                 Person owner = Person.NewTitledInstance("Owner");
 678                 rights.setAgent(owner);
 679
 680                 //source
 681                 IdentifiableSource source = identifiableEntity.addSource(OriginalSourceType.Import, "id", "idNamespace",
 682                                 getReference(), "123");
 683                 source.setOriginalNameString("original name");
 684
 685                 //LSID
 686                  try {
 687                         LSID lsid = new LSID("urn:lsid:a.b.de:namespace:1234");
 688                         identifiableEntity.setLsid(lsid);
 689                 } catch (MalformedLSIDException e) {
 690                         e.printStackTrace();
 691                 }
 692
 693
 694         }
 695
 696
 697         private Reference<?> getReference() {
 698                  Reference<?> result = ReferenceFactory.newGeneric();
 699                  result.setTitle("some generic reference");
 700                  return result;
 701         }
 702
 703
 704         private DerivedUnit getSpecimen() {
 705                 DerivedUnit derivedUnit = DerivedUnit.NewPreservedSpecimenInstance();
 706                 return derivedUnit;
 707         }
 708
 709
 710
 711         private Taxon getTaxon() {
 712                 Reference<?> sec = getReference();
 713                 TaxonNameBase<?,?> name = BotanicalName.NewInstance(Rank.GENUS());
 714                 Taxon taxon = Taxon.NewInstance(name, sec);
 715                 return taxon;
 716
 717         }
 718 }