package eu.etaxonomy.cdm.api.service;
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.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;
import eu.etaxonomy.cdm.model.molecular.DnaSample;
import eu.etaxonomy.cdm.model.molecular.Sequence;
import eu.etaxonomy.cdm.model.molecular.SingleRead;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
-import eu.etaxonomy.cdm.model.occurrence.DerivationEventType;
+import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
-import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationType;
+import eu.etaxonomy.cdm.persistence.dao.molecular.ISingleReadDao;
import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
@SpringBeanByType
private IOccurrenceService occurrenceService;
+ @SpringBeanByType
+ private ISingleReadDao singleReadDao;
+
@SpringBeanByType
private ISequenceService sequenceService;
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
//delete field unit
- deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
+ deleteResult = occurrenceService.delete(fieldUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
//delete derived unit
- deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
+ deleteResult = occurrenceService.delete(derivedUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
//delete dna sample
- deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
+ deleteResult = occurrenceService.delete(dnaSample, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
}
+ @Test
+ @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceDeepDeleteTest.testDeepDelete_SingleRead.xml")
+ public void testDeepDelete_SingleRead(){
+ UUID sequenceA1Uuid = UUID.fromString("3db46d26-94ef-4759-aad8-42d0b9aea9b6");
+ UUID sequenceA2Uuid = UUID.fromString("afa3771c-2b9d-46d7-82e0-8b9c050706e3");
+ UUID sequenceB1Uuid = UUID.fromString("d7199db5-708e-470a-a573-9c760dd07cd1");
+ UUID sequenceB2Uuid = UUID.fromString("1cb83575-38ea-4a8c-9418-d87163f425ce");
+ UUID singleReadAUuid = UUID.fromString("82f538a1-2274-4d55-b27b-ed2f004ab5cd");
+ UUID singleReadBUuid = UUID.fromString("fc74199a-89dc-40a0-9cbd-08cebebff4b5");
+
+ //how the XML was generated
+// Sequence sequenceA1 = Sequence.NewInstance("A");
+// Sequence sequenceA2 = Sequence.NewInstance("T");
+// Sequence sequenceB1 = Sequence.NewInstance("C");
+// Sequence sequenceB2 = Sequence.NewInstance("G");
+//
+// SingleRead singleReadA = SingleRead.NewInstance();
+// SingleRead singleReadB = SingleRead.NewInstance();
+//
+// sequenceA1.setUuid(sequenceA1Uuid);
+// sequenceA2.setUuid(sequenceA2Uuid);
+// sequenceB1.setUuid(sequenceB1Uuid);
+// sequenceB1.setUuid(sequenceB2Uuid);
+// singleReadA.setUuid(singleReadAUuid);
+// singleReadB.setUuid(singleReadBUuid);
+//
+// SingleReadAlignment.NewInstance(sequenceA1, singleReadA);
+// SingleReadAlignment.NewInstance(sequenceA2, singleReadA);
+// SingleReadAlignment.NewInstance(sequenceB1, singleReadB);
+// SingleReadAlignment.NewInstance(sequenceB2, singleReadB);
+//
+// sequenceService.save(sequenceA1);
+// sequenceService.save(sequenceA2);
+// sequenceService.save(sequenceB1);
+// sequenceService.save(sequenceB2);
+//
+// commitAndStartNewTransaction(null);
+//
+// setComplete();
+// endTransaction();
+//
+// try {
+// writeDbUnitDataSetFile(new String[] {
+// "SpecimenOrObservationBase",
+// "SpecimenOrObservationBase_DerivationEvent",
+// "DerivationEvent",
+// "Sequence",
+// "SingleRead",
+// "SingleReadAlignment",
+// "Amplification",
+// "AmplificationResult",
+// "DescriptionElementBase",
+// "DescriptionBase",
+// "TaxonBase",
+// "TypeDesignationBase",
+// "TaxonNameBase",
+// "TaxonNameBase_TypeDesignationBase",
+// "HomotypicalGroup"
+// }, "testDeepDelete_SingleRead");
+// } catch (FileNotFoundException e) {
+// e.printStackTrace();
+// }
+
+ DeleteResult deleteResult = null;
+ SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
+ config.setDeleteMolecularData(true);
+ config.setDeleteChildren(true);
+
+ Sequence sequenceA1 = sequenceService.load(sequenceA1Uuid);
+ Sequence sequenceA2 = sequenceService.load(sequenceA2Uuid);
+ Sequence sequenceB1 = sequenceService.load(sequenceB1Uuid);
+ Sequence sequenceB2 = sequenceService.load(sequenceB2Uuid);
+ SingleRead singleReadA = singleReadDao.load(singleReadAUuid);
+ SingleRead singleReadB = singleReadDao.load(singleReadBUuid);
+
+ //check initial state
+ assertNotNull(sequenceA1);
+ assertNotNull(sequenceA2);
+ assertNotNull(sequenceB1);
+ assertNotNull(sequenceB2);
+ assertNotNull(singleReadA);
+ assertNotNull(singleReadB);
+ assertEquals("number of sequences incorrect", 4, sequenceService.count(Sequence.class));
+ assertEquals("incorrect number of single reads", 2, singleReadDao.count());
+
+ //A: delete singleRead
+ //delete singleReadA from sequenceA1 (singleReadA should NOT be deleted)
+ deleteResult = sequenceService.deleteSingleRead(singleReadA, sequenceA1);
+ assertTrue(deleteResult.toString(), deleteResult.isOk());
+ assertEquals("incorrect number of single reads", 2, singleReadDao.count());
+ assertEquals(0, sequenceA1.getSingleReadAlignments().size());
+ assertNotNull(singleReadDao.load(singleReadAUuid));
+
+ //delete singleReadA from sequenceA2 (singleReadA should be deleted)
+ deleteResult = sequenceService.deleteSingleRead(singleReadA, sequenceA2);
+ assertTrue(deleteResult.toString(), deleteResult.isOk());
+ assertEquals("incorrect number of single reads", 1, singleReadDao.count());
+ assertEquals(0, sequenceA2.getSingleReadAlignments().size());
+ assertTrue(singleReadDao.load(singleReadAUuid)==null);
+
+ //B: delete sequence
+ //delete sequenceB1 (singleReadB should NOT be deleted)
+ deleteResult = sequenceService.delete(sequenceB1Uuid);
+ assertTrue(deleteResult.toString(), deleteResult.isOk());
+ assertEquals("incorrect number of single reads", 1, singleReadDao.count());
+ assertNotNull(singleReadDao.load(singleReadBUuid));
+
+ //delete sequenceB1 (singleReadB should be deleted)
+ deleteResult = sequenceService.delete(sequenceB2Uuid);
+ assertTrue(deleteResult.toString(), deleteResult.isOk());
+ assertEquals("incorrect number of single reads", 0, singleReadDao.count());
+ assertTrue(singleReadDao.load(singleReadBUuid)==null);
+ }
+
@Test
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceDeepDeleteTest.testDeepDelete_FieldUnitWithSiblingDerivatives.xml")
public void testDeepDelete_FieldUnitWithSiblingDerivatives(){
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
//delete field unit
- deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
+ deleteResult = occurrenceService.delete(fieldUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
assertEquals("incorrect number of single reads", 1, consensusSequence.getSingleReads().size());
assertEquals(consensusSequence.getSingleReads().iterator().next(), dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next());
- //delete sequence -> should fail
- deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
- assertFalse(deleteResult.toString(), deleteResult.isOk());
-
//allow deletion of molecular data
config.setDeleteMolecularData(true);
SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
- deleteResult = occurrenceService.deleteSingleRead(singleRead, consensusSequence);
+ deleteResult = sequenceService.deleteSingleRead(singleRead, consensusSequence);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals("incorrect number of single reads", 0, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
assertEquals("incorrect number of single reads", 0, consensusSequence.getSingleReads().size());
+ assertEquals("incorrect number of single reads", 0, singleReadDao.count());
- //delete sequence -> should fail
- deleteResult = occurrenceService.deleteDerivateHierarchy(consensusSequence, config);
+ //delete sequence
+ deleteResult = sequenceService.delete(consensusSequence);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
//delete dna sample
- deleteResult = occurrenceService.deleteDerivateHierarchy(dnaSample, config);
+ deleteResult = occurrenceService.delete(dnaSample, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
//delete tissue sample
- deleteResult = occurrenceService.deleteDerivateHierarchy(tissueSample, config);
+ deleteResult = occurrenceService.delete(tissueSample, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
//delete derived unit
- deleteResult = occurrenceService.deleteDerivateHierarchy(derivedUnit, config);
+ deleteResult = occurrenceService.delete(derivedUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
//delete field unit
- deleteResult = occurrenceService.deleteDerivateHierarchy(fieldUnit, config);
+ deleteResult = occurrenceService.delete(fieldUnit, config);
assertTrue(deleteResult.toString(), deleteResult.isOk());
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
}
@Override
- @Test
- @Ignore
+// @Test
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");
+ UUID sequenceA1Uuid = UUID.fromString("3db46d26-94ef-4759-aad8-42d0b9aea9b6");
+ UUID sequenceA2Uuid = UUID.fromString("afa3771c-2b9d-46d7-82e0-8b9c050706e3");
+ UUID sequenceB1Uuid = UUID.fromString("d7199db5-708e-470a-a573-9c760dd07cd1");
+ UUID sequenceB2Uuid = UUID.fromString("1cb83575-38ea-4a8c-9418-d87163f425ce");
+ UUID singleReadAUuid = UUID.fromString("82f538a1-2274-4d55-b27b-ed2f004ab5cd");
+ UUID singleReadBUuid = UUID.fromString("fc74199a-89dc-40a0-9cbd-08cebebff4b5");
//how the XML was generated
- FieldUnit fieldUnit = FieldUnit.NewInstance();
- fieldUnit.setUuid(FIELD_UNIT_UUID);
- //sub derivates (DerivedUnit, DnaSample)
- DerivedUnit derivedUnit = DerivedUnit.NewInstance(SpecimenOrObservationType.PreservedSpecimen);
- derivedUnit.setUuid(DERIVED_UNIT_UUID);
- DnaSample dnaSample = (DnaSample) DerivedUnit.NewInstance(SpecimenOrObservationType.DnaSample);
- dnaSample.setUuid(DNA_SAMPLE_UUID);
-
- //derivation events
- DerivationEvent.NewSimpleInstance(fieldUnit, derivedUnit, DerivationEventType.ACCESSIONING());
- DerivationEvent.NewSimpleInstance(fieldUnit, dnaSample, DerivationEventType.DNA_EXTRACTION());
-
- occurrenceService.save(fieldUnit);
- occurrenceService.save(derivedUnit);
- occurrenceService.save(dnaSample);
+ Sequence sequenceA1 = Sequence.NewInstance("A");
+ Sequence sequenceA2 = Sequence.NewInstance("T");
+ Sequence sequenceB1 = Sequence.NewInstance("C");
+ Sequence sequenceB2 = Sequence.NewInstance("G");
+
+ SingleRead singleReadA = SingleRead.NewInstance();
+ SingleRead singleReadB = SingleRead.NewInstance();
+
+ sequenceA1.setUuid(sequenceA1Uuid);
+ sequenceA2.setUuid(sequenceA2Uuid);
+ sequenceB1.setUuid(sequenceB1Uuid);
+ sequenceB1.setUuid(sequenceB2Uuid);
+ singleReadA.setUuid(singleReadAUuid);
+ singleReadB.setUuid(singleReadBUuid);
+
+ SingleReadAlignment.NewInstance(sequenceA1, singleReadA);
+ SingleReadAlignment.NewInstance(sequenceA2, singleReadA);
+ SingleReadAlignment.NewInstance(sequenceB1, singleReadB);
+ SingleReadAlignment.NewInstance(sequenceB2, singleReadB);
+
+ sequenceService.save(sequenceA1);
+ sequenceService.save(sequenceA2);
+ sequenceService.save(sequenceB1);
+ sequenceService.save(sequenceB2);
commitAndStartNewTransaction(null);
"TaxonNameBase",
"TaxonNameBase_TypeDesignationBase",
"HomotypicalGroup"
- }, "testDeepDelete_FieldUnitWithSiblingDerivatives");
+ }, "testDeepDelete_SingleRead");
} catch (FileNotFoundException e) {
e.printStackTrace();
}
+
+ System.out.println(sequenceA1.getUuid());
+ System.out.println(sequenceA2.getUuid());
+ System.out.println(sequenceB1.getUuid());
+ System.out.println(sequenceB2.getUuid());
+ System.out.println(singleReadA.getUuid());
+ System.out.println(singleReadB.getUuid());
}
}
BGBM BDI Projects / cdmlib.git / blobdiff