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/**
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* Copyright (C) 2014 EDIT
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* European Distributed Institute of Taxonomy
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* http://www.e-taxonomy.eu
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*
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* The contents of this file are subject to the Mozilla Public License Version 1.1
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* See LICENSE.TXT at the top of this package for the full license terms.
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*/
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package eu.etaxonomy.cdm.api.service;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertNotNull;
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import static org.junit.Assert.assertTrue;
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import java.io.FileNotFoundException;
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import java.util.UUID;
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import org.apache.log4j.Logger;
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import org.junit.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.config.SpecimenDeleteConfigurator;
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import eu.etaxonomy.cdm.api.service.molecular.ISequenceService;
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import eu.etaxonomy.cdm.api.service.pager.Pager;
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import eu.etaxonomy.cdm.model.molecular.DnaSample;
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import eu.etaxonomy.cdm.model.molecular.Sequence;
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import eu.etaxonomy.cdm.model.molecular.SingleRead;
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import eu.etaxonomy.cdm.model.molecular.SingleReadAlignment;
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import eu.etaxonomy.cdm.model.name.NomenclaturalCode;
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import eu.etaxonomy.cdm.model.name.Rank;
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import eu.etaxonomy.cdm.model.name.SpecimenTypeDesignation;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.name.TypeDesignationBase;
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import eu.etaxonomy.cdm.model.occurrence.DerivationEvent;
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit;
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import eu.etaxonomy.cdm.model.occurrence.FieldUnit;
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import eu.etaxonomy.cdm.model.occurrence.GatheringEvent;
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import eu.etaxonomy.cdm.model.occurrence.SpecimenOrObservationBase;
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import eu.etaxonomy.cdm.persistence.dao.molecular.ISingleReadDao;
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import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
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import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
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/**
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* @author pplitzner
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* @since 31.03.2014
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*
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*/
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public class OccurrenceServiceDeepDeleteTest extends CdmTransactionalIntegrationTest {
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private final UUID FIELD_UNIT_UUID = UUID.fromString("b5f58da5-4442-4001-9d13-33f41518b72a");
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private final UUID DERIVED_UNIT_UUID = UUID.fromString("448be6e7-f19c-4a10-9a0a-97aa005f817d");
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private final UUID DNA_SAMPLE_UUID = UUID.fromString("bee4212b-aff1-484e-845f-065c7d6216af");
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private final UUID SEQUENCE_UUID = UUID.fromString("0b867369-de8c-4837-a708-5b7d9f6091be");
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private final UUID FIELD_UNIT2_UUID = UUID.fromString("ae798108-6483-4d09-900f-7f849c43bcc9");
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@SuppressWarnings("unused")
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private static final Logger logger = Logger.getLogger(OccurrenceServiceDeepDeleteTest.class);
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@SpringBeanByType
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private IOccurrenceService occurrenceService;
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@SpringBeanByType
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private IEventBaseService eventService;
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@SpringBeanByType
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private ISingleReadDao singleReadDao;
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@SpringBeanByType
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private ISequenceService sequenceService;
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@SpringBeanByType
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private INameService nameService;
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml")
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public void testDeepDelete_FieldUnit(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
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GatheringEvent gatheringEvent = GatheringEvent.NewInstance();
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fieldUnit.setGatheringEvent(gatheringEvent);
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FieldUnit fieldUnit2 = (FieldUnit) occurrenceService.load(FIELD_UNIT2_UUID);
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fieldUnit2.setGatheringEvent(gatheringEvent);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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//check initial state
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assertEquals(assertMessage, 6, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 4, eventService.count(DerivationEvent.class));
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assertEquals(assertMessage, 2, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 4, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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assertEquals("incorrect number of gathering events", 1, eventService.count(GatheringEvent.class));
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//delete field unit
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deleteResult = occurrenceService.delete(fieldUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 2, eventService.count(DerivationEvent.class));
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of gathering events", 1, eventService.count(GatheringEvent.class));
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deleteResult = occurrenceService.delete(fieldUnit2, config);
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assertEquals(assertMessage, 0, eventService.count(GatheringEvent.class));
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceTest.testDeleteDerivateHierarchyStepByStep.xml")
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public void testDeepDelete_FieldUnitWithTypeDesignation(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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config.setDeleteFromTypeDesignation(true);
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FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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TaxonName name = TaxonName.NewInstance(NomenclaturalCode.ICNAFP, Rank.SPECIES(), "Test", null, "test", null, null, null, null, null);
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SpecimenTypeDesignation specimenTypeDesignation = SpecimenTypeDesignation.NewInstance();
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specimenTypeDesignation.setTypeSpecimen(dnaSample);
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name.addTypeDesignation(specimenTypeDesignation, false);
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nameService.save(name);
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Pager<TypeDesignationBase> typeDesignations = nameService.getTypeDesignations(name, null, 100, 0);
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Long oldCount= typeDesignations.getCount();
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//check initial state
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assertEquals(assertMessage, 6, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 4, eventService.count(DerivationEvent.class));
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assertEquals(assertMessage, 2, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 4, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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//delete field unit
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deleteResult = occurrenceService.delete(fieldUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 2, eventService.count(DerivationEvent.class));
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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typeDesignations = nameService.getTypeDesignations(name, null, 100, 0);
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Long afterDeleteCount= typeDesignations.getCount();
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assertTrue(oldCount > afterDeleteCount);
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeepDelete_DerivedUnit(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(DERIVED_UNIT_UUID);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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//check initial state
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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//delete derived unit
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deleteResult = occurrenceService.delete(derivedUnit, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testDeepDelete_DnaSample(){
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String assertMessage = "Incorrect number of specimens after deletion.";
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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DnaSample dnaSample = (DnaSample) occurrenceService.load(DNA_SAMPLE_UUID);
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//check initial state
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assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
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assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
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assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
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assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
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//delete dna sample
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deleteResult = occurrenceService.delete(dnaSample, config);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
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assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
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assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
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assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceDeepDeleteTest.testDeepDelete_SingleRead.xml")
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public void testDeepDelete_SingleRead(){
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UUID sequenceA1Uuid = UUID.fromString("3db46d26-94ef-4759-aad8-42d0b9aea9b6");
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UUID sequenceA2Uuid = UUID.fromString("afa3771c-2b9d-46d7-82e0-8b9c050706e3");
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UUID sequenceB1Uuid = UUID.fromString("d7199db5-708e-470a-a573-9c760dd07cd1");
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UUID sequenceB2Uuid = UUID.fromString("1cb83575-38ea-4a8c-9418-d87163f425ce");
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UUID singleReadAUuid = UUID.fromString("82f538a1-2274-4d55-b27b-ed2f004ab5cd");
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UUID singleReadBUuid = UUID.fromString("fc74199a-89dc-40a0-9cbd-08cebebff4b5");
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//how the XML was generated
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// Sequence sequenceA1 = Sequence.NewInstance("A");
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// Sequence sequenceA2 = Sequence.NewInstance("T");
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// Sequence sequenceB1 = Sequence.NewInstance("C");
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// Sequence sequenceB2 = Sequence.NewInstance("G");
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//
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// SingleRead singleReadA = SingleRead.NewInstance();
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// SingleRead singleReadB = SingleRead.NewInstance();
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//
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// sequenceA1.setUuid(sequenceA1Uuid);
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// sequenceA2.setUuid(sequenceA2Uuid);
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// sequenceB1.setUuid(sequenceB1Uuid);
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// sequenceB1.setUuid(sequenceB2Uuid);
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// singleReadA.setUuid(singleReadAUuid);
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// singleReadB.setUuid(singleReadBUuid);
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//
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// SingleReadAlignment.NewInstance(sequenceA1, singleReadA);
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// SingleReadAlignment.NewInstance(sequenceA2, singleReadA);
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// SingleReadAlignment.NewInstance(sequenceB1, singleReadB);
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// SingleReadAlignment.NewInstance(sequenceB2, singleReadB);
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//
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// sequenceService.save(sequenceA1);
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// sequenceService.save(sequenceA2);
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// sequenceService.save(sequenceB1);
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// sequenceService.save(sequenceB2);
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//
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// commitAndStartNewTransaction(null);
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//
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// setComplete();
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// endTransaction();
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//
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// try {
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// writeDbUnitDataSetFile(new String[] {
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// "SpecimenOrObservationBase",
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// "SpecimenOrObservationBase_DerivationEvent",
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// "DerivationEvent",
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// "Sequence",
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// "SingleRead",
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// "SingleReadAlignment",
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// "Amplification",
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// "AmplificationResult",
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// "DescriptionElementBase",
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// "DescriptionBase",
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// "TaxonBase",
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// "TypeDesignationBase",
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// "TaxonName",
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// "TaxonName_TypeDesignationBase",
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// "HomotypicalGroup"
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// }, "testDeepDelete_SingleRead");
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// } catch (FileNotFoundException e) {
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// e.printStackTrace();
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// }
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DeleteResult deleteResult = null;
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SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
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config.setDeleteMolecularData(true);
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config.setDeleteChildren(true);
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Sequence sequenceA1 = sequenceService.load(sequenceA1Uuid);
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Sequence sequenceA2 = sequenceService.load(sequenceA2Uuid);
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Sequence sequenceB1 = sequenceService.load(sequenceB1Uuid);
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Sequence sequenceB2 = sequenceService.load(sequenceB2Uuid);
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SingleRead singleReadA = singleReadDao.load(singleReadAUuid);
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SingleRead singleReadB = singleReadDao.load(singleReadBUuid);
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//check initial state
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assertNotNull(sequenceA1);
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assertNotNull(sequenceA2);
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assertNotNull(sequenceB1);
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assertNotNull(sequenceB2);
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assertNotNull(singleReadA);
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assertNotNull(singleReadB);
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assertEquals("number of sequences incorrect", 4, sequenceService.count(Sequence.class));
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assertEquals("incorrect number of single reads", 2, singleReadDao.count());
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//A: delete singleRead
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//delete singleReadA from sequenceA1 (singleReadA should NOT be deleted)
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deleteResult = sequenceService.deleteSingleRead(singleReadA, sequenceA1);
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assertTrue(deleteResult.toString(), deleteResult.isOk());
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assertEquals("incorrect number of single reads", 2, singleReadDao.count());
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312
|
assertEquals(0, sequenceA1.getSingleReadAlignments().size());
|
|
313
|
assertNotNull(singleReadDao.load(singleReadAUuid));
|
|
314
|
|
|
315
|
//delete singleReadA from sequenceA2 (singleReadA should be deleted)
|
|
316
|
deleteResult = sequenceService.deleteSingleRead(singleReadA, sequenceA2);
|
|
317
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
318
|
assertEquals("incorrect number of single reads", 1, singleReadDao.count());
|
|
319
|
assertEquals(0, sequenceA2.getSingleReadAlignments().size());
|
|
320
|
assertTrue(singleReadDao.load(singleReadAUuid)==null);
|
|
321
|
|
|
322
|
//B: delete sequence
|
|
323
|
//delete sequenceB1 (singleReadB should NOT be deleted)
|
|
324
|
deleteResult = sequenceService.delete(sequenceB1Uuid);
|
|
325
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
326
|
assertEquals("incorrect number of single reads", 1, singleReadDao.count());
|
|
327
|
assertNotNull(singleReadDao.load(singleReadBUuid));
|
|
328
|
|
|
329
|
//delete sequenceB1 (singleReadB should be deleted)
|
|
330
|
deleteResult = sequenceService.delete(sequenceB2Uuid);
|
|
331
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
332
|
assertEquals("incorrect number of single reads", 0, singleReadDao.count());
|
|
333
|
assertTrue(singleReadDao.load(singleReadBUuid)==null);
|
|
334
|
}
|
|
335
|
|
|
336
|
@Test
|
|
337
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="OccurrenceServiceDeepDeleteTest.testDeepDelete_FieldUnitWithSiblingDerivatives.xml")
|
|
338
|
public void testDeepDelete_FieldUnitWithSiblingDerivatives(){
|
|
339
|
String assertMessage = "Incorrect number of specimens after deletion.";
|
|
340
|
DeleteResult deleteResult = null;
|
|
341
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
342
|
config.setDeleteChildren(true);
|
|
343
|
|
|
344
|
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(FIELD_UNIT_UUID);
|
|
345
|
|
|
346
|
//check initial state
|
|
347
|
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
348
|
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
|
|
349
|
assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
|
|
350
|
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
|
|
351
|
|
|
352
|
//delete field unit
|
|
353
|
deleteResult = occurrenceService.delete(fieldUnit, config);
|
|
354
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
355
|
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
356
|
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
|
|
357
|
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
|
|
358
|
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
|
|
359
|
}
|
|
360
|
|
|
361
|
|
|
362
|
@Test
|
|
363
|
@DataSet(value="OccurrenceServiceDeepDeleteTest.testDeleteStepByStep.xml", loadStrategy=CleanSweepInsertLoadStrategy.class)
|
|
364
|
public void testDeleteDerivateHierarchyStepByStep(){
|
|
365
|
UUID fieldUnitUuid = UUID.fromString("4d91a9bc-2af7-40f8-b6e6-545305301807");
|
|
366
|
UUID derivedUnitUuid = UUID.fromString("f9c57904-e512-4927-90ad-f3833cdef967");
|
|
367
|
UUID tissueSampleUuid = UUID.fromString("14b92fce-1236-455b-ba46-2a7e35d9230e");
|
|
368
|
UUID dnaSampleUuid = UUID.fromString("60c31688-edec-4796-aa2f-28a7ea12256b");
|
|
369
|
UUID sequenceUuid = UUID.fromString("24804b67-d6f7-48e5-811a-e7240230d305");
|
|
370
|
|
|
371
|
String assertMessage = "Incorrect number of specimens after deletion.";
|
|
372
|
DeleteResult deleteResult = null;
|
|
373
|
SpecimenDeleteConfigurator config = new SpecimenDeleteConfigurator();
|
|
374
|
|
|
375
|
FieldUnit fieldUnit = (FieldUnit) occurrenceService.load(fieldUnitUuid);
|
|
376
|
DerivedUnit derivedUnit = (DerivedUnit) occurrenceService.load(derivedUnitUuid);
|
|
377
|
DerivedUnit tissueSample = (DerivedUnit) occurrenceService.load(tissueSampleUuid);
|
|
378
|
DnaSample dnaSample = (DnaSample) occurrenceService.load(dnaSampleUuid);
|
|
379
|
Sequence consensusSequence = sequenceService.load(sequenceUuid);
|
|
380
|
|
|
381
|
//check initial state
|
|
382
|
assertNotNull(fieldUnit);
|
|
383
|
assertNotNull(derivedUnit);
|
|
384
|
assertNotNull(tissueSample);
|
|
385
|
assertNotNull(dnaSample);
|
|
386
|
assertNotNull(consensusSequence);
|
|
387
|
|
|
388
|
assertEquals(assertMessage, 4, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
389
|
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
|
|
390
|
assertEquals(assertMessage, 3, occurrenceService.count(DerivedUnit.class));
|
|
391
|
assertEquals(assertMessage, 1, occurrenceService.count(DnaSample.class));
|
|
392
|
assertEquals("incorrect number of amplification results", 1, dnaSample.getAmplificationResults().size());
|
|
393
|
assertEquals("number of sequences incorrect", 1, dnaSample.getSequences().size());
|
|
394
|
assertEquals("incorrect number of single reads", 1, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
|
|
395
|
assertEquals("incorrect number of single reads", 1, consensusSequence.getSingleReads().size());
|
|
396
|
assertEquals(consensusSequence.getSingleReads().iterator().next(), dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next());
|
|
397
|
|
|
398
|
//allow deletion of molecular data
|
|
399
|
config.setDeleteMolecularData(true);
|
|
400
|
|
|
401
|
SingleRead singleRead = dnaSample.getAmplificationResults().iterator().next().getSingleReads().iterator().next();
|
|
402
|
deleteResult = sequenceService.deleteSingleRead(singleRead, consensusSequence);
|
|
403
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
404
|
assertEquals("incorrect number of single reads", 0, dnaSample.getAmplificationResults().iterator().next().getSingleReads().size());
|
|
405
|
assertEquals("incorrect number of single reads", 0, consensusSequence.getSingleReads().size());
|
|
406
|
assertEquals("incorrect number of single reads", 0, singleReadDao.count());
|
|
407
|
|
|
408
|
//delete sequence
|
|
409
|
deleteResult = sequenceService.delete(consensusSequence);
|
|
410
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
411
|
assertEquals("number of sequences incorrect", 0, dnaSample.getSequences().size());
|
|
412
|
|
|
413
|
|
|
414
|
//delete dna sample
|
|
415
|
deleteResult = occurrenceService.delete(dnaSample, config);
|
|
416
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
417
|
assertEquals(assertMessage, 3, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
418
|
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
|
|
419
|
assertEquals(assertMessage, 2, occurrenceService.count(DerivedUnit.class));
|
|
420
|
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
|
|
421
|
|
|
422
|
//delete tissue sample
|
|
423
|
deleteResult = occurrenceService.delete(tissueSample, config);
|
|
424
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
425
|
assertEquals(assertMessage, 2, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
426
|
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
|
|
427
|
assertEquals(assertMessage, 1, occurrenceService.count(DerivedUnit.class));
|
|
428
|
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
|
|
429
|
|
|
430
|
//delete derived unit
|
|
431
|
deleteResult = occurrenceService.delete(derivedUnit, config);
|
|
432
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
433
|
assertEquals(assertMessage, 1, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
434
|
assertEquals(assertMessage, 1, occurrenceService.count(FieldUnit.class));
|
|
435
|
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
|
|
436
|
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
|
|
437
|
|
|
438
|
//delete field unit
|
|
439
|
deleteResult = occurrenceService.delete(fieldUnit, config);
|
|
440
|
|
|
441
|
assertTrue(deleteResult.toString(), deleteResult.isOk());
|
|
442
|
assertEquals(assertMessage, 0, occurrenceService.count(SpecimenOrObservationBase.class));
|
|
443
|
assertEquals(assertMessage, 0, occurrenceService.count(FieldUnit.class));
|
|
444
|
assertEquals(assertMessage, 0, occurrenceService.count(DerivedUnit.class));
|
|
445
|
assertEquals(assertMessage, 0, occurrenceService.count(DnaSample.class));
|
|
446
|
}
|
|
447
|
|
|
448
|
@Override
|
|
449
|
// @Test
|
|
450
|
public void createTestDataSet() throws FileNotFoundException {
|
|
451
|
UUID sequenceA1Uuid = UUID.fromString("3db46d26-94ef-4759-aad8-42d0b9aea9b6");
|
|
452
|
UUID sequenceA2Uuid = UUID.fromString("afa3771c-2b9d-46d7-82e0-8b9c050706e3");
|
|
453
|
UUID sequenceB1Uuid = UUID.fromString("d7199db5-708e-470a-a573-9c760dd07cd1");
|
|
454
|
UUID sequenceB2Uuid = UUID.fromString("1cb83575-38ea-4a8c-9418-d87163f425ce");
|
|
455
|
UUID singleReadAUuid = UUID.fromString("82f538a1-2274-4d55-b27b-ed2f004ab5cd");
|
|
456
|
UUID singleReadBUuid = UUID.fromString("fc74199a-89dc-40a0-9cbd-08cebebff4b5");
|
|
457
|
|
|
458
|
//how the XML was generated
|
|
459
|
Sequence sequenceA1 = Sequence.NewInstance("A");
|
|
460
|
Sequence sequenceA2 = Sequence.NewInstance("T");
|
|
461
|
Sequence sequenceB1 = Sequence.NewInstance("C");
|
|
462
|
Sequence sequenceB2 = Sequence.NewInstance("G");
|
|
463
|
|
|
464
|
SingleRead singleReadA = SingleRead.NewInstance();
|
|
465
|
SingleRead singleReadB = SingleRead.NewInstance();
|
|
466
|
|
|
467
|
sequenceA1.setUuid(sequenceA1Uuid);
|
|
468
|
sequenceA2.setUuid(sequenceA2Uuid);
|
|
469
|
sequenceB1.setUuid(sequenceB1Uuid);
|
|
470
|
sequenceB1.setUuid(sequenceB2Uuid);
|
|
471
|
singleReadA.setUuid(singleReadAUuid);
|
|
472
|
singleReadB.setUuid(singleReadBUuid);
|
|
473
|
|
|
474
|
SingleReadAlignment.NewInstance(sequenceA1, singleReadA);
|
|
475
|
SingleReadAlignment.NewInstance(sequenceA2, singleReadA);
|
|
476
|
SingleReadAlignment.NewInstance(sequenceB1, singleReadB);
|
|
477
|
SingleReadAlignment.NewInstance(sequenceB2, singleReadB);
|
|
478
|
|
|
479
|
sequenceService.save(sequenceA1);
|
|
480
|
sequenceService.save(sequenceA2);
|
|
481
|
sequenceService.save(sequenceB1);
|
|
482
|
sequenceService.save(sequenceB2);
|
|
483
|
|
|
484
|
commitAndStartNewTransaction(null);
|
|
485
|
|
|
486
|
setComplete();
|
|
487
|
endTransaction();
|
|
488
|
|
|
489
|
try {
|
|
490
|
writeDbUnitDataSetFile(new String[] {
|
|
491
|
"SpecimenOrObservationBase",
|
|
492
|
"SpecimenOrObservationBase_DerivationEvent",
|
|
493
|
"DerivationEvent",
|
|
494
|
"Sequence",
|
|
495
|
"SingleRead",
|
|
496
|
"SingleReadAlignment",
|
|
497
|
"Amplification",
|
|
498
|
"AmplificationResult",
|
|
499
|
"DescriptionElementBase",
|
|
500
|
"DescriptionBase",
|
|
501
|
"TaxonBase",
|
|
502
|
"TypeDesignationBase",
|
|
503
|
"TaxonName",
|
|
504
|
"TaxonName_TypeDesignationBase",
|
|
505
|
"HomotypicalGroup"
|
|
506
|
}, "testDeepDelete_SingleRead", true);
|
|
507
|
} catch (FileNotFoundException e) {
|
|
508
|
e.printStackTrace();
|
|
509
|
}
|
|
510
|
|
|
511
|
System.out.println(sequenceA1.getUuid());
|
|
512
|
System.out.println(sequenceA2.getUuid());
|
|
513
|
System.out.println(sequenceB1.getUuid());
|
|
514
|
System.out.println(sequenceB2.getUuid());
|
|
515
|
System.out.println(singleReadA.getUuid());
|
|
516
|
System.out.println(singleReadB.getUuid());
|
|
517
|
}
|
|
518
|
}
|