Revision 88b4ec59
Added by Patrick Plitzner over 9 years ago
- extracted deepDelete tests to own java class
- reduced exception logged in DeleteResult
| cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/OccurrenceServiceTest.java | ||
|---|---|---|
| 74 | 74 |
*/ |
| 75 | 75 |
public class OccurrenceServiceTest extends CdmTransactionalIntegrationTest {
|
| 76 | 76 |
|
| 77 |
private static final UUID FIELD_UNIT_UUID = UUID.fromString("b5f58da5-4442-4001-9d13-33f41518b72a");
|
|
| 78 |
private static final UUID DERIVED_UNIT_UUID = UUID.fromString("448be6e7-f19c-4a10-9a0a-97aa005f817d");
|
|
| 79 |
private static final UUID DNA_SAMPLE_UUID = UUID.fromString("bee4212b-aff1-484e-845f-065c7d6216af");
|
|
| 80 |
private static final UUID SEQUENCE_UUID = UUID.fromString("0b867369-de8c-4837-a708-5b7d9f6091be");
|
|
| 81 |
private static final UUID TAXON_UUID = UUID.fromString("e93b3840-326c-446e-89f1-a7611f17c0e8");
|
|
| 82 |
private static final UUID TAXON_DESCRIPTION_UUID = UUID.fromString("a87a893e-2ea8-427d-a26b-dbd2515d6b8a");
|
|
| 83 |
private static final UUID BOTANICAL_NAME_UUID = UUID.fromString("a604774e-d66a-4d47-b9d1-d0e38a8c787a");
|
|
| 84 |
|
|
| 85 | 77 |
@SuppressWarnings("unused")
|
| 86 | 78 |
private static final Logger logger = Logger.getLogger(OccurrenceServiceTest.class); |
| 87 | 79 |
|
| ... | ... | |
| 244 | 236 |
@Test |
| 245 | 237 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteIndividualAssociatedAndTypeSpecimen.xml") |
| 246 | 238 |
public void testDeleteIndividualAssociatedAndTypeSpecimen(){
|
| 247 |
// //how the XML was generated |
|
| 239 |
final UUID taxonDEscriptionUuid = UUID.fromString("a87a893e-2ea8-427d-a26b-dbd2515d6b8a");
|
|
| 240 |
final UUID botanicalNameUuid = UUID.fromString("a604774e-d66a-4d47-b9d1-d0e38a8c787a");
|
|
| 241 |
final UUID fieldUnitUuid = UUID.fromString("67e81ca8-ff91-4df6-bf48-e4600c7f15a2");
|
|
| 242 |
final UUID derivedUnitUuid = UUID.fromString("d229713b-0123-4f15-bffc-76ae45c37564");
|
|
| 243 |
|
|
| 244 |
// //how the XML was generated |
|
| 248 | 245 |
// FieldUnit fieldUnit = FieldUnit.NewInstance(); |
| 249 |
// fieldUnit.setUuid(FIELD_UNIT_UUID);
|
|
| 246 |
// fieldUnit.setUuid(fieldUnitUuid);
|
|
| 250 | 247 |
// //sub derivates (DerivedUnit, DnaSample) |
| 251 | 248 |
// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 252 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID);
|
|
| 249 |
// derivedUnit.setUuid(derivedUnitUuid);
|
|
| 253 | 250 |
// |
| 254 | 251 |
// //derivation events |
| 255 |
// DerivationEvent derivationEventFUtoDU = DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
|
|
| 252 |
// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING()); |
|
| 256 | 253 |
// |
| 257 | 254 |
// occurrenceService.save(fieldUnit); |
| 258 | 255 |
// occurrenceService.save(derivedUnit); |
| ... | ... | |
| 269 | 266 |
// // IndividualsAssociations and a "described" voucher specimen, and an |
| 270 | 267 |
// // empty one) |
| 271 | 268 |
// Taxon taxon = Taxon.NewInstance(name, null); |
| 272 |
// taxon.setUuid(TAXON_UUID);
|
|
| 269 |
// taxon.setUuid(taxonUuid);
|
|
| 273 | 270 |
// TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
| 274 | 271 |
// taxonDescription.setUuid(TAXON_DESCRIPTION_UUID); |
| 275 | 272 |
// //add voucher |
| ... | ... | |
| 307 | 304 |
// e.printStackTrace(); |
| 308 | 305 |
// } |
| 309 | 306 |
|
| 310 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
|
|
| 311 |
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
|
|
| 312 |
BotanicalName name = (BotanicalName) nameService.load(BOTANICAL_NAME_UUID);
|
|
| 313 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(TAXON_DESCRIPTION_UUID);
|
|
| 307 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
| 308 |
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
| 309 |
BotanicalName name = (BotanicalName) nameService.load(botanicalNameUuid);
|
|
| 310 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDEscriptionUuid);
|
|
| 314 | 311 |
//check initial state (IndividualsAssociation) |
| 315 | 312 |
DescriptionElementBase descriptionElement = taxonDescription.getElements().iterator().next(); |
| 316 | 313 |
assertTrue("wrong type of description element", descriptionElement.isInstanceOf(IndividualsAssociation.class));
|
| 317 | 314 |
assertEquals("associated specimen is incorrect", associatedFieldUnit, ((IndividualsAssociation)descriptionElement).getAssociatedSpecimenOrObservation());
|
| 318 | 315 |
//check initial state (Type Designation) |
| 319 | 316 |
Set<TypeDesignationBase> typeDesignations = name.getTypeDesignations(); |
| 320 |
TypeDesignationBase typeDesignation = typeDesignations.iterator().next(); |
|
| 317 |
TypeDesignationBase<?> typeDesignation = typeDesignations.iterator().next();
|
|
| 321 | 318 |
assertTrue("wrong type of type designation", typeDesignation.isInstanceOf(SpecimenTypeDesignation.class));
|
| 322 | 319 |
assertEquals("type specimen is incorrect", typeSpecimen, ((SpecimenTypeDesignation)typeDesignation).getTypeSpecimen());
|
| 323 | 320 |
|
| ... | ... | |
| 348 | 345 |
} |
| 349 | 346 |
|
| 350 | 347 |
@Test |
| 351 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml") |
|
| 352 |
public void testDeepDelete_FieldUnit(){
|
|
| 353 |
String assertMessage = "Incorrect number of specimens after deletion."; |
|
| 354 |
DeleteResult deleteResult = null; |
|
| 355 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
|
| 356 |
config.setDeleteMolecularData(true); |
|
| 357 |
config.setDeleteChildren(true); |
|
| 358 |
|
|
| 359 |
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID); |
|
| 360 |
DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID); |
|
| 361 |
|
|
| 362 |
//check initial state |
|
| 363 |
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 364 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 365 |
assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class)); |
|
| 366 |
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class)); |
|
| 367 |
assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
|
|
| 368 |
assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
|
|
| 369 |
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
|
|
| 370 |
|
|
| 371 |
//delete field unit |
|
| 372 |
deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config); |
|
| 373 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 374 |
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 375 |
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class)); |
|
| 376 |
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class)); |
|
| 377 |
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class)); |
|
| 378 |
} |
|
| 379 |
|
|
| 380 |
@Test |
|
| 381 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml") |
|
| 382 |
public void testDeepDelete_DerivedUnit(){
|
|
| 383 |
String assertMessage = "Incorrect number of specimens after deletion."; |
|
| 384 |
DeleteResult deleteResult = null; |
|
| 385 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
|
| 386 |
config.setDeleteMolecularData(true); |
|
| 387 |
config.setDeleteChildren(true); |
|
| 388 |
|
|
| 389 |
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID); |
|
| 390 |
DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID); |
|
| 391 |
|
|
| 392 |
//check initial state |
|
| 393 |
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 394 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 395 |
assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class)); |
|
| 396 |
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class)); |
|
| 397 |
assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
|
|
| 398 |
assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
|
|
| 399 |
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
|
|
| 400 |
|
|
| 401 |
//delete derived unit |
|
| 402 |
deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config); |
|
| 403 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 404 |
assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 405 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 406 |
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class)); |
|
| 407 |
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class)); |
|
| 408 |
} |
|
| 409 |
|
|
| 410 |
@Test |
|
| 411 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml") |
|
| 412 |
public void testDeepDelete_DnaSample(){
|
|
| 413 |
String assertMessage = "Incorrect number of specimens after deletion."; |
|
| 414 |
DeleteResult deleteResult = null; |
|
| 415 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
|
| 416 |
config.setDeleteMolecularData(true); |
|
| 417 |
config.setDeleteChildren(true); |
|
| 418 |
|
|
| 419 |
DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID); |
|
| 420 |
|
|
| 421 |
//check initial state |
|
| 422 |
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 423 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 424 |
assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class)); |
|
| 425 |
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class)); |
|
| 426 |
assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
|
|
| 427 |
assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
|
|
| 428 |
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
|
|
| 429 |
|
|
| 430 |
//delete dna sample |
|
| 431 |
deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config); |
|
| 432 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 433 |
assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 434 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 435 |
assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class)); |
|
| 436 |
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class)); |
|
| 437 |
} |
|
| 438 |
|
|
| 439 |
|
|
| 440 |
@Test |
|
| 441 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml") |
|
| 442 |
public void testDeleteDerivateHierarchyStepByStep(){
|
|
| 443 |
// //how the XML was generated |
|
| 444 |
// FieldUnit fieldUnit = FieldUnit.NewInstance(); |
|
| 445 |
// fieldUnit.setUuid(FIELD_UNIT_UUID); |
|
| 446 |
// //sub derivates (DerivedUnit, DnaSample) |
|
| 447 |
// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
|
| 448 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID); |
|
| 449 |
// DnaSample dnaSample = DnaSample.NewInstance(); |
|
| 450 |
// dnaSample.setUuid(DNA_SAMPLE_UUID); |
|
| 451 |
// |
|
| 452 |
// //derivation events |
|
| 453 |
// DerivationEvent derivationEventFUtoDU = DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING()); |
|
| 454 |
// DerivationEvent derivationEventDUtoDNA = DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION()); |
|
| 455 |
// |
|
| 456 |
// //DNA (Sequence, SingleRead, Amplification) |
|
| 457 |
// Sequence sequence = Sequence.NewInstance(dnaSample, "ATTCG", 5); |
|
| 458 |
// sequence.setUuid(SEQUENCE_UUID); |
|
| 459 |
// SingleRead singleRead = SingleRead.NewInstance(); |
|
| 460 |
// sequence.addSingleRead(singleRead); |
|
| 461 |
// dnaSample.addSequence(sequence); |
|
| 462 |
// AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample); |
|
| 463 |
// amplificationResult.addSingleRead(singleRead); |
|
| 464 |
// occurrenceService.save(fieldUnit); |
|
| 465 |
// occurrenceService.save(derivedUnit); |
|
| 466 |
// occurrenceService.save(dnaSample); |
|
| 467 |
// |
|
| 468 |
// commitAndStartNewTransaction(null); |
|
| 469 |
// |
|
| 470 |
// setComplete(); |
|
| 471 |
// endTransaction(); |
|
| 472 |
// |
|
| 473 |
// |
|
| 474 |
// try {
|
|
| 475 |
// writeDbUnitDataSetFile(new String[] {
|
|
| 476 |
// "SpecimenOrObservationBase", |
|
| 477 |
// "SpecimenOrObservationBase_DerivationEvent", |
|
| 478 |
// "DerivationEvent", |
|
| 479 |
// "Sequence", |
|
| 480 |
// "Sequence_SingleRead", |
|
| 481 |
// "SingleRead", |
|
| 482 |
// "AmplificationResult" |
|
| 483 |
// }, "testDeleteDerivateHierarchyStepByStep"); |
|
| 484 |
// } catch (FileNotFoundException e) {
|
|
| 485 |
// e.printStackTrace(); |
|
| 486 |
// } |
|
| 487 |
|
|
| 488 |
|
|
| 489 |
String assertMessage = "Incorrect number of specimens after deletion."; |
|
| 490 |
DeleteResult deleteResult = null; |
|
| 491 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
|
| 492 |
|
|
| 493 |
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID); |
|
| 494 |
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID); |
|
| 495 |
DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID); |
|
| 496 |
Sequence consensusSequence = sequenceService.load(SEQUENCE_UUID); |
|
| 497 |
|
|
| 498 |
//check initial state |
|
| 499 |
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 500 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 501 |
assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class)); |
|
| 502 |
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class)); |
|
| 503 |
assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
|
|
| 504 |
assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
|
|
| 505 |
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
|
|
| 506 |
|
|
| 507 |
//delete single read -> should fail |
|
| 508 |
SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next(); |
|
| 509 |
deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config); |
|
| 510 |
assertFalse(deleteResult.toString(), deleteResult.isOk()); |
|
| 511 |
//delete sequence -> should fail |
|
| 512 |
deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config); |
|
| 513 |
assertFalse(deleteResult.toString(), deleteResult.isOk()); |
|
| 514 |
|
|
| 515 |
//allow deletion of molecular data |
|
| 516 |
config.setDeleteMolecularData(true); |
|
| 517 |
|
|
| 518 |
deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config); |
|
| 519 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 520 |
assertTrue(consensusSequence.getSingleReads().isEmpty()); |
|
| 521 |
|
|
| 522 |
//delete sequence -> should fail |
|
| 523 |
deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config); |
|
| 524 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 525 |
assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
|
|
| 526 |
|
|
| 527 |
|
|
| 528 |
//delete dna sample |
|
| 529 |
deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config); |
|
| 530 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 531 |
assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 532 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 533 |
assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class)); |
|
| 534 |
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class)); |
|
| 535 |
|
|
| 536 |
//delete derived unit |
|
| 537 |
deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config); |
|
| 538 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 539 |
assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 540 |
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class)); |
|
| 541 |
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class)); |
|
| 542 |
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class)); |
|
| 543 |
|
|
| 544 |
//delete field unit |
|
| 545 |
deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config); |
|
| 546 |
deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config); |
|
| 547 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
|
| 548 |
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class)); |
|
| 549 |
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class)); |
|
| 550 |
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class)); |
|
| 551 |
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class)); |
|
| 552 |
} |
|
| 553 |
|
|
| 554 |
@Test |
|
| 555 |
@DataSet |
|
| 348 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testListAssociatedAndTypedTaxa.xml") |
|
| 556 | 349 |
public void testListAssociatedAndTypedTaxa(){
|
| 350 |
UUID fieldUnitUuid = UUID.fromString("b359ff20-98de-46bf-aa43-3e10bb072cd4");
|
|
| 351 |
UUID typeSpecimenUuid = UUID.fromString("0f8608c7-ffe7-40e6-828c-cb3382580878");
|
|
| 352 |
UUID taxonDescriptionUuid = UUID.fromString("d77db2d4-45a1-4aa1-ab34-f33395f54965");
|
|
| 353 |
UUID taxonUuid = UUID.fromString("b0de794c-8cb7-4369-8f83-870ca37abbe0");
|
|
| 557 | 354 |
// //how the XML was generated |
| 558 | 355 |
// FieldUnit associatedFieldUnit = FieldUnit.NewInstance(); |
| 356 |
// associatedFieldUnit.setUuid(fieldUnitUuid); |
|
| 559 | 357 |
// //sub derivates (DerivedUnit, DnaSample) |
| 560 | 358 |
// DerivedUnit typeSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 561 |
// DerivedUnit voucherSpecimen = DerivedUnit.NewInstance(SpecimenOrObservationType.HumanObservation); |
|
| 562 |
// DnaSample dnaSample = DnaSample.NewInstance(); |
|
| 563 |
// //description for voucher specimen (with InidividualsAssociation to type specimen just to make it complex ;) ) |
|
| 564 |
// SpecimenDescription voucherSpecimenDescription = SpecimenDescription.NewInstance(voucherSpecimen); |
|
| 565 |
// voucherSpecimenDescription.addElement(IndividualsAssociation.NewInstance(typeSpecimen)); |
|
| 359 |
// typeSpecimen.setUuid(typeSpecimenUuid); |
|
| 566 | 360 |
// |
| 567 | 361 |
// //derivation events |
| 568 | 362 |
// DerivationEvent.NewSimpleInstance(associatedFieldUnit, typeSpecimen, DerivationEventType.ACCESSIONING()); |
| 569 |
// DerivationEvent.NewSimpleInstance(associatedFieldUnit, voucherSpecimen, DerivationEventType.ACCESSIONING()); |
|
| 570 |
// DerivationEvent.NewSimpleInstance(typeSpecimen, dnaSample, DerivationEventType.DNA_EXTRACTION()); |
|
| 571 | 363 |
// |
| 572 |
// //DNA (Sequence, SingleRead, Amplification) |
|
| 573 |
// Sequence consensusSequence = Sequence.NewInstance(dnaSample, "ATTCG", 5); |
|
| 574 |
// SingleRead singleRead = SingleRead.NewInstance(); |
|
| 575 |
// consensusSequence.addSingleRead(singleRead); |
|
| 576 |
// dnaSample.addSequence(consensusSequence); |
|
| 577 |
// Amplification amplification = Amplification.NewInstance(dnaSample); |
|
| 578 |
// amplification.addSingleRead(singleRead); |
|
| 579 | 364 |
// occurrenceService.save(associatedFieldUnit); |
| 580 | 365 |
// occurrenceService.save(typeSpecimen); |
| 581 |
// occurrenceService.save(dnaSample); |
|
| 582 | 366 |
// |
| 583 | 367 |
// //create name with type specimen |
| 584 | 368 |
// BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
|
| ... | ... | |
| 589 | 373 |
// // IndividualsAssociations and a "described" voucher specimen, and an |
| 590 | 374 |
// // empty one) |
| 591 | 375 |
// Taxon taxon = Taxon.NewInstance(name, null); |
| 376 |
// taxon.setUuid(taxonUuid); |
|
| 592 | 377 |
// TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
| 378 |
// taxonDescription.setUuid(taxonDescriptionUuid); |
|
| 593 | 379 |
// //add voucher |
| 594 |
// taxonDescription.setDescribedSpecimenOrObservation(voucherSpecimen); |
|
| 595 | 380 |
// taxonDescription.addElement(IndividualsAssociation.NewInstance(associatedFieldUnit)); |
| 596 | 381 |
// taxon.addDescription(taxonDescription); |
| 597 | 382 |
// //add type designation to name |
| ... | ... | |
| 600 | 385 |
// taxon.addDescription(TaxonDescription.NewInstance()); |
| 601 | 386 |
// taxonService.saveOrUpdate(taxon); |
| 602 | 387 |
// |
| 388 |
// commitAndStartNewTransaction(null); |
|
| 603 | 389 |
// |
| 604 |
// commitAndStartNewTransaction(new String[]{"SpecimenOrObservationBase",
|
|
| 605 |
// "SpecimenOrObservationBase_DerivationEvent", |
|
| 606 |
// "DerivationEvent", |
|
| 607 |
// "Sequence", |
|
| 608 |
// "Sequence_SingleRead", |
|
| 609 |
// "SingleRead", |
|
| 610 |
// "Amplification", |
|
| 611 |
// "Amplification_SingleRead", |
|
| 612 |
// "DescriptionElementBase", |
|
| 613 |
// "DescriptionBase", |
|
| 614 |
// "TaxonBase", |
|
| 615 |
// "TypeDesignationBase", |
|
| 616 |
// "TaxonNameBase", |
|
| 617 |
// "TaxonNameBase_TypeDesignationBase", |
|
| 618 |
// "HomotypicalGroup"}); |
|
| 390 |
// setComplete(); |
|
| 391 |
// endTransaction(); |
|
| 392 |
// |
|
| 393 |
// try {
|
|
| 394 |
// writeDbUnitDataSetFile(new String[]{
|
|
| 395 |
// "SpecimenOrObservationBase", |
|
| 396 |
// "SpecimenOrObservationBase_DerivationEvent", |
|
| 397 |
// "DerivationEvent", |
|
| 398 |
// "Sequence", |
|
| 399 |
// "Sequence_SingleRead", |
|
| 400 |
// "SingleRead", |
|
| 401 |
// "AmplificationResult", |
|
| 402 |
// "DescriptionElementBase", |
|
| 403 |
// "DescriptionBase", |
|
| 404 |
// "TaxonBase", |
|
| 405 |
// "TypeDesignationBase", |
|
| 406 |
// "TaxonNameBase", |
|
| 407 |
// "TaxonNameBase_TypeDesignationBase", |
|
| 408 |
// "HomotypicalGroup"}, "testListAssociatedAndTypedTaxa"); |
|
| 409 |
// } catch (FileNotFoundException e) {
|
|
| 410 |
// // TODO Auto-generated catch block |
|
| 411 |
// e.printStackTrace(); |
|
| 412 |
// } |
|
| 619 | 413 |
// |
| 620 | 414 |
// System.out.println("associatedFieldUnit.getUuid() " + associatedFieldUnit.getUuid());
|
| 621 | 415 |
// System.out.println("typeSpecimen.getUuid() "+typeSpecimen.getUuid());
|
| 622 |
// System.out.println("voucherSpecimen.getUuid() "+voucherSpecimen.getUuid());
|
|
| 623 | 416 |
// System.out.println("taxonDescription.getUuid() "+taxonDescription.getUuid());
|
| 417 |
// System.out.println("taxon.getUuid() "+taxon.getUuid());
|
|
| 624 | 418 |
|
| 625 | 419 |
|
| 626 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
|
|
| 627 |
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
|
|
| 628 |
Taxon taxon = (Taxon) taxonService.load(TAXON_UUID);
|
|
| 629 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(TAXON_DESCRIPTION_UUID);
|
|
| 420 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
| 421 |
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(typeSpecimenUuid);
|
|
| 422 |
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
|
| 423 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
|
|
| 630 | 424 |
//check for FieldUnit (IndividualsAssociation) |
| 631 | 425 |
java.util.Collection<IndividualsAssociation> individualsAssociations = occurrenceService.listIndividualsAssociations(associatedFieldUnit, null, null, null,null); |
| 632 | 426 |
assertEquals("Number of individuals associations is incorrect", 1, individualsAssociations.size());
|
| ... | ... | |
| 643 | 437 |
SpecimenTypeDesignation specimenTypeDesignation = typeDesignations.iterator().next(); |
| 644 | 438 |
Set<TaxonNameBase> typifiedNames = specimenTypeDesignation.getTypifiedNames(); |
| 645 | 439 |
assertEquals("number of typified names is incorrect", 1, typifiedNames.size());
|
| 646 |
Set taxonBases = typifiedNames.iterator().next().getTaxonBases(); |
|
| 440 |
Set<?> taxonBases = typifiedNames.iterator().next().getTaxonBases();
|
|
| 647 | 441 |
assertEquals("number of taxa incorrect", 1, taxonBases.size());
|
| 648 | 442 |
Object next = taxonBases.iterator().next(); |
| 649 | 443 |
assertTrue(next instanceof CdmBase && ((CdmBase)next).isInstanceOf(Taxon.class)); |
| ... | ... | |
| 653 | 447 |
@Test |
| 654 | 448 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithSpecimenDescription.xml") |
| 655 | 449 |
public void testIsDeletableWithSpecimenDescription(){
|
| 450 |
UUID derivedUnitUuid = UUID.fromString("68095c8e-025d-49f0-8bb2-ed36378b75c3");
|
|
| 451 |
UUID specimenDescriptionUuid = UUID.fromString("4094f947-ce84-47b1-bad5-e57e33239d3c");
|
|
| 656 | 452 |
// //how the XML was generated |
| 657 | 453 |
// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 658 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID);
|
|
| 454 |
// derivedUnit.setUuid(derivedUnitUuid);
|
|
| 659 | 455 |
// SpecimenDescription specimenDescription = SpecimenDescription.NewInstance(); |
| 456 |
// specimenDescription.setUuid(specimenDescriptionUuid); |
|
| 660 | 457 |
// derivedUnit.addDescription(specimenDescription); |
| 661 | 458 |
// occurrenceService.save(derivedUnit); |
| 662 | 459 |
// |
| ... | ... | |
| 687 | 484 |
// } |
| 688 | 485 |
|
| 689 | 486 |
|
| 690 |
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
|
|
| 691 |
SpecimenDescription specimenDescription = (SpecimenDescription) derivedUnit.getDescriptions().iterator().next();
|
|
| 487 |
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
| 488 |
SpecimenDescription specimenDescription = (SpecimenDescription) descriptionService.load(specimenDescriptionUuid);
|
|
| 692 | 489 |
|
| 693 | 490 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
| 694 | 491 |
DeleteResult deleteResult = null; |
| ... | ... | |
| 706 | 503 |
@Test |
| 707 | 504 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithDescribedSpecimenInTaxonDescription.xml") |
| 708 | 505 |
public void testIsDeletableWithDescribedSpecimenInTaxonDescription(){
|
| 506 |
UUID fieldUnitUuid = UUID.fromString("d656a004-38ee-404c-810a-87ffb0ab16c2");
|
|
| 709 | 507 |
// //how the XML was generated |
| 710 | 508 |
// FieldUnit fieldUnit = FieldUnit.NewInstance(); |
| 711 |
// fieldUnit.setUuid(FIELD_UNIT_UUID);
|
|
| 509 |
// fieldUnit.setUuid(fieldUnitUuid);
|
|
| 712 | 510 |
// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 713 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID); |
|
| 714 | 511 |
// |
| 715 | 512 |
// //derivation events |
| 716 | 513 |
// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING()); |
| ... | ... | |
| 721 | 518 |
// // create taxon with name and two taxon descriptions |
| 722 | 519 |
// //(one with a "described" voucher specimen, and an empty one) |
| 723 | 520 |
// Taxon taxon = Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."), null);
|
| 724 |
// taxon.setUuid(TAXON_UUID); |
|
| 725 |
// TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
|
| 726 |
// taxonDescription.setUuid(TAXON_DESCRIPTION_UUID); |
|
| 521 |
// taxonDescription.setUuid(taxonDescriptionUuid); |
|
| 727 | 522 |
// //add voucher |
| 728 | 523 |
// taxonDescription.setDescribedSpecimenOrObservation(derivedUnit); |
| 729 | 524 |
// taxon.addDescription(taxonDescription); |
| ... | ... | |
| 759 | 554 |
// e.printStackTrace(); |
| 760 | 555 |
// } |
| 761 | 556 |
|
| 762 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID); |
|
| 763 |
|
|
| 764 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(TAXON_DESCRIPTION_UUID); |
|
| 557 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid); |
|
| 765 | 558 |
|
| 766 | 559 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
| 767 | 560 |
DeleteResult deleteResult = null; |
| ... | ... | |
| 779 | 572 |
@Test |
| 780 | 573 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithIndividualsAssociationTaxonDescription.xml") |
| 781 | 574 |
public void testIsDeletableWithIndividualsAssociationTaxonDescription(){
|
| 575 |
UUID fieldUnitUuid = UUID.fromString("7978b978-5100-4c7a-82ef-3a23e0f3c723");
|
|
| 576 |
UUID taxonDescriptionUuid = UUID.fromString("d4b0d561-6e7e-4fd8-bf3c-925530f949eb");
|
|
| 782 | 577 |
// //how the XML was generated |
| 783 | 578 |
// FieldUnit fieldUnit = FieldUnit.NewInstance(); |
| 784 |
// fieldUnit.setUuid(FIELD_UNIT_UUID);
|
|
| 579 |
// fieldUnit.setUuid(fieldUnitUuid);
|
|
| 785 | 580 |
// |
| 786 | 581 |
// occurrenceService.save(fieldUnit); |
| 787 | 582 |
// |
| ... | ... | |
| 789 | 584 |
// // IndividualsAssociations and a "described" voucher specimen, and an |
| 790 | 585 |
// // empty one) |
| 791 | 586 |
// Taxon taxon = Taxon.NewInstance(BotanicalName.PARSED_NAME("Campanula patual sec L."), null);
|
| 792 |
// taxon.setUuid(TAXON_UUID); |
|
| 793 | 587 |
// TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
| 794 |
// taxonDescription.setUuid(TAXON_DESCRIPTION_UUID);
|
|
| 588 |
// taxonDescription.setUuid(taxonDescriptionUuid);
|
|
| 795 | 589 |
// //add voucher |
| 796 | 590 |
// taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit)); |
| 797 | 591 |
// taxon.addDescription(taxonDescription); |
| ... | ... | |
| 827 | 621 |
// e.printStackTrace(); |
| 828 | 622 |
// } |
| 829 | 623 |
|
| 830 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
|
|
| 831 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(TAXON_DESCRIPTION_UUID);
|
|
| 624 |
FieldUnit associatedFieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
| 625 |
TaxonDescription taxonDescription = (TaxonDescription) descriptionService.load(taxonDescriptionUuid);
|
|
| 832 | 626 |
IndividualsAssociation individualsAssociation = (IndividualsAssociation) taxonDescription.getElements().iterator().next(); |
| 833 | 627 |
|
| 834 | 628 |
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator(); |
| ... | ... | |
| 849 | 643 |
@Test |
| 850 | 644 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithTypeDesignation.xml") |
| 851 | 645 |
public void testIsDeletableWithTypeDesignation(){
|
| 646 |
UUID derivedUnitUuid = UUID.fromString("f7fd1dc1-3c93-42a7-8279-cde5bfe37ea0");
|
|
| 647 |
UUID botanicalNameUuid = UUID.fromString("7396430c-c932-4dd3-a45a-40c2808b132e");
|
|
| 852 | 648 |
// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 853 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID);
|
|
| 649 |
//// derivedUnit.setUuid(derivedUnitUuid);
|
|
| 854 | 650 |
// |
| 855 | 651 |
// occurrenceService.save(derivedUnit); |
| 856 | 652 |
// |
| 857 | 653 |
// //create name with type specimen |
| 858 | 654 |
// BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
|
| 859 |
// name.setUuid(BOTANICAL_NAME_UUID);
|
|
| 655 |
//// name.setUuid(botanicalNameUuid);
|
|
| 860 | 656 |
// SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance(); |
| 861 | 657 |
// typeDesignation.setTypeSpecimen(derivedUnit); |
| 862 | 658 |
// //add type designation to name |
| ... | ... | |
| 893 | 689 |
|
| 894 | 690 |
|
| 895 | 691 |
|
| 896 |
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
|
|
| 692 |
DerivedUnit typeSpecimen = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
| 897 | 693 |
|
| 898 | 694 |
//create name with type specimen |
| 899 |
BotanicalName name = (BotanicalName) nameService.load(BOTANICAL_NAME_UUID);
|
|
| 695 |
BotanicalName name = (BotanicalName) nameService.load(botanicalNameUuid);
|
|
| 900 | 696 |
SpecimenTypeDesignation typeDesignation = (SpecimenTypeDesignation) name.getTypeDesignations().iterator().next(); |
| 901 | 697 |
|
| 902 | 698 |
//add type designation to name |
| ... | ... | |
| 921 | 717 |
@Test |
| 922 | 718 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testIsDeletableWithChildren.xml") |
| 923 | 719 |
public void testIsDeletableWithChildren(){
|
| 720 |
UUID fieldUnitUuid = UUID.fromString("92ada058-4c14-4131-8ecd-b82dc1dd2882");
|
|
| 721 |
UUID derivedUnitUuid = UUID.fromString("896dffdc-6809-4914-8950-5501fee1c0fd");
|
|
| 722 |
UUID dnaSampleUuid = UUID.fromString("7efd1d66-ac7f-4202-acdf-a72cbb9c3a21");
|
|
| 924 | 723 |
// //how the XML was generated |
| 925 | 724 |
// FieldUnit fieldUnit = FieldUnit.NewInstance(); |
| 926 |
// fieldUnit.setUuid(FIELD_UNIT_UUID);
|
|
| 725 |
//// fieldUnit.setUuid(fieldUnitUuid);
|
|
| 927 | 726 |
// //sub derivates (DerivedUnit, DnaSample) |
| 928 | 727 |
// DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 929 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID);
|
|
| 728 |
//// derivedUnit.setUuid(derivedUnitUuid);
|
|
| 930 | 729 |
// DnaSample dnaSample = DnaSample.NewInstance(); |
| 931 |
// dnaSample.setUuid(DNA_SAMPLE_UUID);
|
|
| 730 |
//// dnaSample.setUuid(dnaSampleUuid);
|
|
| 932 | 731 |
// |
| 933 | 732 |
// //derivation events |
| 934 |
// DerivationEvent derivationEventFUtoDU = DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
|
|
| 935 |
// DerivationEvent derivationEventDUtoDNA = DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
|
|
| 733 |
// DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING()); |
|
| 734 |
// DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION()); |
|
| 936 | 735 |
// |
| 937 | 736 |
// occurrenceService.save(fieldUnit); |
| 938 | 737 |
// occurrenceService.save(derivedUnit); |
| ... | ... | |
| 964 | 763 |
// } catch (FileNotFoundException e) {
|
| 965 | 764 |
// e.printStackTrace(); |
| 966 | 765 |
// } |
| 967 |
|
|
| 968 |
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID); |
|
| 766 |
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid); |
|
| 969 | 767 |
//sub derivates (DerivedUnit, DnaSample) |
| 970 |
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID); |
|
| 971 |
DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID); |
|
| 768 |
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid); |
|
| 769 |
DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid); |
|
| 770 |
// Sequence sequence = dnaSample.getSequences().iterator().next(); |
|
| 771 |
|
|
| 972 | 772 |
//derivation events |
| 973 | 773 |
DerivationEvent fieldUnitToDerivedUnitEvent = fieldUnit.getDerivationEvents().iterator().next(); |
| 974 | 774 |
DerivationEvent derivedUnitToDnaSampleEvent = derivedUnit.getDerivationEvents().iterator().next(); |
| ... | ... | |
| 978 | 778 |
DeleteResult deleteResult = null; |
| 979 | 779 |
//check deletion of DnaSample |
| 980 | 780 |
deleteResult = occurrenceService.isDeletable(dnaSample, config); |
| 981 |
assertFalse(deleteResult.toString(), deleteResult.isOk()); |
|
| 982 |
//allow deletion of molecular data |
|
| 983 |
config.setDeleteMolecularData(true); |
|
| 984 |
deleteResult = occurrenceService.isDeletable(dnaSample, config); |
|
| 985 | 781 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
| 986 |
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent)); |
|
| 987 | 782 |
|
| 988 | 783 |
//check deletion of Specimen |
| 989 | 784 |
deleteResult = occurrenceService.isDeletable(derivedUnit, config); |
| 990 | 785 |
assertFalse(deleteResult.toString(), deleteResult.isOk()); |
| 991 | 786 |
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(derivedUnitToDnaSampleEvent)); |
| 992 |
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(fieldUnitToDerivedUnitEvent)); |
|
| 993 | 787 |
|
| 994 | 788 |
//delete DnaSample |
| 995 | 789 |
occurrenceService.deleteDerivateHierarchy(dnaSample, config); |
| 996 | 790 |
|
| 997 | 791 |
deleteResult = occurrenceService.isDeletable(derivedUnit, config); |
| 998 | 792 |
assertTrue(deleteResult.toString(), deleteResult.isOk()); |
| 999 |
assertTrue(deleteResult.toString(), deleteResult.getRelatedObjects().contains(fieldUnitToDerivedUnitEvent)); |
|
| 1000 | 793 |
|
| 1001 | 794 |
//check deletion of fieldUnit |
| 1002 | 795 |
deleteResult = occurrenceService.isDeletable(fieldUnit, config); |
| ... | ... | |
| 1017 | 810 |
public void createTestDataSet() throws FileNotFoundException {
|
| 1018 | 811 |
//how the XML was generated |
| 1019 | 812 |
FieldUnit fieldUnit = FieldUnit.NewInstance(); |
| 1020 |
fieldUnit.setUuid(FIELD_UNIT_UUID); |
|
| 813 |
// fieldUnit.setUuid(FIELD_UNIT_UUID);
|
|
| 1021 | 814 |
//sub derivates (DerivedUnit, DnaSample) |
| 1022 | 815 |
DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil); |
| 1023 |
derivedUnit.setUuid(DERIVED_UNIT_UUID); |
|
| 816 |
// derivedUnit.setUuid(DERIVED_UNIT_UUID);
|
|
| 1024 | 817 |
DnaSample dnaSample = DnaSample.NewInstance(); |
| 1025 |
dnaSample.setUuid(DNA_SAMPLE_UUID); |
|
| 818 |
// dnaSample.setUuid(DNA_SAMPLE_UUID);
|
|
| 1026 | 819 |
|
| 1027 | 820 |
//derivation events |
| 1028 |
DerivationEvent derivationEventFUtoDU = DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
|
|
| 1029 |
DerivationEvent derivationEventDUtoDNA = DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
|
|
| 821 |
DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING()); |
|
| 822 |
DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION()); |
|
| 1030 | 823 |
|
| 1031 | 824 |
//DNA (Sequence, SingleRead, Amplification) |
| 1032 | 825 |
Sequence sequence = Sequence.NewInstance(dnaSample, "ATTCG", 5); |
| 1033 |
sequence.setUuid(SEQUENCE_UUID); |
|
| 826 |
// sequence.setUuid(SEQUENCE_UUID);
|
|
| 1034 | 827 |
SingleRead singleRead = SingleRead.NewInstance(); |
| 1035 | 828 |
sequence.addSingleRead(singleRead); |
| 1036 | 829 |
dnaSample.addSequence(sequence); |
| ... | ... | |
| 1042 | 835 |
|
| 1043 | 836 |
//create name with type specimen |
| 1044 | 837 |
BotanicalName name = BotanicalName.PARSED_NAME("Campanula patual sec L.");
|
| 1045 |
name.setUuid(BOTANICAL_NAME_UUID); |
|
| 838 |
// name.setUuid(BOTANICAL_NAME_UUID);
|
|
| 1046 | 839 |
SpecimenTypeDesignation typeDesignation = SpecimenTypeDesignation.NewInstance(); |
| 1047 | 840 |
typeDesignation.setTypeSpecimen(derivedUnit); |
| 1048 | 841 |
//add type designation to name |
| ... | ... | |
| 1052 | 845 |
// IndividualsAssociations and a "described" voucher specimen, and an |
| 1053 | 846 |
// empty one) |
| 1054 | 847 |
Taxon taxon = Taxon.NewInstance(name, null); |
| 1055 |
taxon.setUuid(TAXON_UUID); |
|
| 848 |
// taxon.setUuid(TAXON_UUID);
|
|
| 1056 | 849 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(); |
| 1057 |
taxonDescription.setUuid(TAXON_DESCRIPTION_UUID); |
|
| 850 |
// taxonDescription.setUuid(TAXON_DESCRIPTION_UUID);
|
|
| 1058 | 851 |
//add voucher |
| 1059 | 852 |
taxonDescription.addElement(IndividualsAssociation.NewInstance(fieldUnit)); |
| 1060 | 853 |
taxon.addDescription(taxonDescription); |
Also available in: Unified diff