import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import java.io.FileNotFoundException;
import java.util.UUID;
import org.apache.log4j.Logger;
-import org.junit.Ignore;
import org.junit.Test;
import org.unitils.dbunit.annotation.DataSet;
import org.unitils.spring.annotation.SpringBeanByType;
private final UUID DERIVED_UNIT_UUID = UUID.fromString("448be6e7-f19c-4a10-9a0a-97aa005f817d");
private final UUID DNA_SAMPLE_UUID = UUID.fromString("bee4212b-aff1-484e-845f-065c7d6216af");
private final UUID SEQUENCE_UUID = UUID.fromString("0b867369-de8c-4837-a708-5b7d9f6091be");
- private final UUID TAXON_UUID = UUID.fromString("e93b3840-326c-446e-89f1-a7611f17c0e8");
@SuppressWarnings("unused")
private static final Logger logger = Logger.getLogger(OccurrenceServiceDeepDeleteTest.class);
@Test
- @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
+ @DataSet(value="OccurrenceServiceDeepDeleteTest.testDeleteStepByStep.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
public void testDeleteDerivateHierarchyStepByStep(){
+ UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
+ UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
+ UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
+ UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
+ UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
+
String assertMessage = "Incorrect number of specimens after deletion.";
DeleteResult deleteResult = null;
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
- FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
- DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
- DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
- Sequence consensusSequence = sequenceService.load(SEQUENCE_UUID);
+ FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
+ DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
+ DerivedUnit tissueSample = (DerivedUnit) occurrenceService.load(tissueSampleUuid);
+ DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);
+ Sequence consensusSequence = sequenceService.load(sequenceUuid);
//check initial state
- assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
+ assertNotNull(fieldUnit);
+ assertNotNull(derivedUnit);
+ assertNotNull(tissueSample);
+ assertNotNull(dnaSample);
+ assertNotNull(consensusSequence);
+
+ assertEquals(assertMessage, 4, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
- assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
+ assertEquals(assertMessage, 3, occurrenceService.count(DerivedUnit.class));
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
+ assertEquals("incorrect number of single reads", 1, consensusSequence.getSingleReads().size());
+ assertEquals(consensusSequence.getSingleReads().iterator().next(), dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next());
- //delete single read -> should fail
- SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
- deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config);
- assertFalse(deleteResult.toString(), deleteResult.isOk());
//delete sequence -> should fail
deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
assertFalse(deleteResult.toString(), deleteResult.isOk());
//allow deletion of molecular data
config.setDeleteMolecularData(true);
- deleteResult = occurrenceService.deleteDerivateHierarchy(singleRead, config);
+ SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
+ deleteResult = occurrenceService.deleteSingleRead(singleRead, consensusSequence);
assertTrue(deleteResult.toString(), deleteResult.isOk());
- assertTrue(consensusSequence.getSingleReads().isEmpty());
+ assertEquals("incorrect number of single reads", 0, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
+ assertEquals("incorrect number of single reads", 0, consensusSequence.getSingleReads().size());
//delete sequence -> should fail
deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
//delete dna sample
deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
+ assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
+ assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
+ assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
+ assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
+
+ //delete tissue sample
+ deleteResult = occurrenceService.deleteDerivateHierarchy(tissueSample, config);
+ assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
//delete field unit
deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
- deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
+
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
}
- /* (non-Javadoc)
- * @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
- */
@Override
@Test
- @Ignore
+// @Ignore
public void createTestDataSet() throws FileNotFoundException {
+ UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
+ UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
+ UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
+ UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
+ UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
+
//how the XML was generated
FieldUnit fieldUnit = FieldUnit.NewInstance();
- fieldUnit.setUuid(FIELD_UNIT_UUID);
+ fieldUnit.setUuid(fieldUnitUuid);
//sub derivates (DerivedUnit, DnaSample)
- DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.Fossil);
- derivedUnit.setUuid(DERIVED_UNIT_UUID);
- DnaSample dnaSample = DnaSample.NewInstance();
- dnaSample.setUuid(DNA_SAMPLE_UUID);
+ DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
+ derivedUnit.setUuid(derivedUnitUuid);
+ DerivedUnit tissueSample = DerivedUnit.NewInstance(SpecimenOrObservationType.TissueSample);
+ tissueSample.setUuid(tissueSampleUuid);
+ DnaSample dnaSample = (DnaSample) DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
+ dnaSample.setUuid(dnaSampleUuid);
+ Sequence sequence = Sequence.NewInstance("");
+ sequence.setUuid(sequenceUuid);
+ SingleRead singleRead1 = SingleRead.NewInstance();
+
+ dnaSample.addSequence(sequence);
+ sequence.addSingleRead(singleRead1);
+ AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample);
+ amplificationResult.addSingleRead(singleRead1);
//derivation events
DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
- DerivationEvent.NewSimpleInstance(derivedUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
+ DerivationEvent.NewSimpleInstance(derivedUnit, tissueSample, DerivationEventType.TISSUE_SAMPLING());
+ DerivationEvent.NewSimpleInstance(tissueSample, dnaSample, DerivationEventType.DNA_EXTRACTION());
- //DNA (Sequence, SingleRead, Amplification)
- Sequence sequence = Sequence.NewInstance(dnaSample, "ATTCG", 5);
- sequence.setUuid(SEQUENCE_UUID);
- SingleRead singleRead = SingleRead.NewInstance();
- sequence.addSingleRead(singleRead);
- dnaSample.addSequence(sequence);
- AmplificationResult amplificationResult = AmplificationResult.NewInstance(dnaSample);
- amplificationResult.addSingleRead(singleRead);
occurrenceService.save(fieldUnit);
occurrenceService.save(derivedUnit);
+ occurrenceService.save(tissueSample);
occurrenceService.save(dnaSample);
commitAndStartNewTransaction(null);
setComplete();
endTransaction();
-
try {
writeDbUnitDataSetFile(new String[] {
"SpecimenOrObservationBase",
"SpecimenOrObservationBase_DerivationEvent",
"DerivationEvent",
"Sequence",
- "Sequence_SingleRead",
"SingleRead",
- "AmplificationResult"
- });
+ "SingleReadAlignment",
+ "Amplification",
+ "AmplificationResult",
+ "DescriptionElementBase",
+ "DescriptionBase",
+ "TaxonBase",
+ "TypeDesignationBase",
+ "TaxonNameBase",
+ "TaxonNameBase_TypeDesignationBase",
+ "HomotypicalGroup"
+ }, "testDeleteStepByStep");
} catch (FileNotFoundException e) {
e.printStackTrace();
}
BGBM BDI Projects / cdmlib.git / blobdiff