Revision 79fadb72
Added by Andreas Müller over 2 years ago
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/description/DescriptiveDataSetServiceTest.java | ||
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/** |
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* Copyright (C) 2021 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.description; |
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import static org.junit.Assert.assertEquals; |
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import static org.junit.Assert.assertTrue; |
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import java.io.FileNotFoundException; |
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import java.math.BigDecimal; |
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import java.util.ArrayList; |
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import java.util.HashSet; |
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import java.util.Iterator; |
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import java.util.List; |
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import java.util.Set; |
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import java.util.UUID; |
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import java.util.stream.Collectors; |
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import org.apache.log4j.Logger; |
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import org.junit.Assert; |
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import org.junit.Before; |
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import org.junit.Ignore; |
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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.dbunit.annotation.DataSets; |
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import org.unitils.spring.annotation.SpringBeanByType; |
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import eu.etaxonomy.cdm.api.application.ICdmRepository; |
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import eu.etaxonomy.cdm.api.service.IClassificationService; |
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import eu.etaxonomy.cdm.api.service.IDescriptionService; |
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import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService; |
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import eu.etaxonomy.cdm.api.service.IReferenceService; |
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import eu.etaxonomy.cdm.api.service.ITaxonNodeService; |
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import eu.etaxonomy.cdm.api.service.ITaxonService; |
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import eu.etaxonomy.cdm.api.service.ITermService; |
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import eu.etaxonomy.cdm.api.service.ITermTreeService; |
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import eu.etaxonomy.cdm.api.service.IVocabularyService; |
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import eu.etaxonomy.cdm.api.service.UpdateResult; |
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import eu.etaxonomy.cdm.api.service.dto.CategoricalDataDto; |
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import eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto; |
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import eu.etaxonomy.cdm.api.service.dto.DescriptionElementDto; |
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import eu.etaxonomy.cdm.api.service.dto.QuantitativeDataDto; |
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import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO; |
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import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO; |
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import eu.etaxonomy.cdm.api.service.dto.StateDataDto; |
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import eu.etaxonomy.cdm.api.service.dto.StatisticalMeasurementValueDto; |
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import eu.etaxonomy.cdm.common.JvmLimitsException; |
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import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
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import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
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import eu.etaxonomy.cdm.model.common.CdmBase; |
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import eu.etaxonomy.cdm.model.description.CategoricalData; |
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import eu.etaxonomy.cdm.model.description.DescriptionBase; |
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
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import eu.etaxonomy.cdm.model.description.DescriptionType; |
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import eu.etaxonomy.cdm.model.description.DescriptiveDataSet; |
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import eu.etaxonomy.cdm.model.description.Feature; |
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import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
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import eu.etaxonomy.cdm.model.description.QuantitativeData; |
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import eu.etaxonomy.cdm.model.description.SpecimenDescription; |
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import eu.etaxonomy.cdm.model.description.State; |
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import eu.etaxonomy.cdm.model.description.StateData; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
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import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
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import eu.etaxonomy.cdm.model.description.TaxonDescription; |
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import eu.etaxonomy.cdm.model.name.IBotanicalName; |
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import eu.etaxonomy.cdm.model.name.Rank; |
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import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
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import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
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import eu.etaxonomy.cdm.model.reference.Reference; |
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import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
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import eu.etaxonomy.cdm.model.taxon.Classification; |
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import eu.etaxonomy.cdm.model.taxon.Taxon; |
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import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
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import eu.etaxonomy.cdm.model.term.TermNode; |
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import eu.etaxonomy.cdm.model.term.TermTree; |
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import eu.etaxonomy.cdm.model.term.TermType; |
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import eu.etaxonomy.cdm.model.term.TermVocabulary; |
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import eu.etaxonomy.cdm.persistence.dto.FeatureDto; |
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import eu.etaxonomy.cdm.persistence.dto.TermDto; |
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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 k.luther |
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* @since 01.10.2021 |
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*/ |
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public class DescriptiveDataSetServiceTest extends CdmTransactionalIntegrationTest { |
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@SuppressWarnings("unused") |
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private static Logger logger = Logger.getLogger(DescriptiveDataSetServiceTest.class); |
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private static final UUID T_LAPSANA_UUID = UUID.fromString("f65d47bd-4f49-4ab1-bc4a-bc4551eaa1a8"); |
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private static final UUID TN_LAPSANA_UUID = UUID.fromString("f4d29e9f-6484-4184-af2e-9704e96a17e3"); |
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private static final UUID T_LAPSANA_COMMUNIS_UUID = UUID.fromString("2a5ceebb-4830-4524-b330-78461bf8cb6b"); |
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private static final UUID T_LAPSANA_COMMUNIS_COMMUNIS_UUID = UUID.fromString("441a3c40-0c84-11de-8c30-0800200c9a66"); |
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private static final UUID T_LAPSANA_COMMUNIS_ADENOPHORA_UUID = UUID.fromString("e4acf200-63b6-11dd-ad8b-0800200c9a66"); |
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private static final UUID T_LAPSANA_COMMUNIS_ALPINA_UUID = UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2"); |
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private static final UUID CLASSIFICATION_UUID = UUID.fromString("4b266053-a841-4980-b548-3f21d8d7d712"); |
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private static final UUID uuidFeatureLeafPA = UUID.fromString("c4dfd16f-f2ed-45e0-8f4d-7fe1ae880510"); |
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private static UUID uuidFeatureLeafLength = UUID.fromString("3c19b50b-4a8e-467e-b7d4-89ebc05a33e1"); |
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private static UUID uuidFeatureLeafColor = UUID.fromString("1e8f503c-5aeb-4788-b4f9-84128f7141c7"); |
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private static UUID uuidLeafColorBlue = UUID.fromString("9b4df19d-f89d-4788-9d71-d1f6f7cae910"); |
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private static UUID uuidLeafColorYellow = UUID.fromString("4cf0881b-0e7b-489a-9fdb-adbe6ae4e0ae"); |
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private static UUID uuidFeatureTree = UUID.fromString("c8a29a94-2754-4d78-9faa-dff3e1387b2d"); |
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@SpringBeanByType |
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private ICdmRepository repository; |
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@SpringBeanByType |
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private ITermService termService; |
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@SpringBeanByType |
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private ITermTreeService termTreeService; |
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@SpringBeanByType |
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private IVocabularyService vocabularyService; |
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@SpringBeanByType |
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private IDescriptionService descriptionService; |
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@SpringBeanByType |
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private ITaxonService taxonService; |
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@SpringBeanByType |
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private ITaxonNodeService taxonNodeService; |
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@SpringBeanByType |
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private IClassificationService classificationService; |
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@SpringBeanByType |
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private IReferenceService referenceService; |
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@SpringBeanByType |
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private IDescriptiveDataSetService datasetService; |
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private StructuredDescriptionAggregation engine; |
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private IProgressMonitor monitor; |
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@Before |
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public void setUp() { |
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// engine.setBatchMinFreeHeap(100 * 1024 * 1024); |
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monitor = DefaultProgressMonitor.NewInstance(); |
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} |
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@Test |
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@DataSets({ |
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), |
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@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), |
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@DataSet(value="StructuredDescriptionAggregationTest.xml"), |
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}) |
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public void testGetRowWrapper(){ |
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createDefaultFeatureTree(); |
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DescriptiveDataSet dataSet = createTestDataset(); |
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commitAndStartNewTransaction(); |
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List<RowWrapperDTO<?>> result = datasetService.getRowWrapper(dataSet.getUuid(), monitor); |
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//There are 4 specimen descriptions and one literature description (taxon association) |
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assertTrue(result.size() == 5); |
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//check rowWrapper |
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//specimen_1 2 categorical and 1 quantitative |
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for (RowWrapperDTO row: result){ |
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if (row instanceof SpecimenRowWrapperDTO){ |
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SpecimenRowWrapperDTO specimen = (SpecimenRowWrapperDTO)row; |
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if (specimen.getSpecimenDto().getLabel().equals("alpina specimen1")){ |
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Set<DescriptionElementDto> elements = specimen.getDataValueForFeature(uuidFeatureLeafColor); |
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if (elements != null && !elements.isEmpty() ){ |
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Iterator<DescriptionElementDto> it = elements.iterator(); |
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DescriptionElementDto dto = null; |
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if (it.hasNext()){ |
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dto = it.next(); |
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}else{ |
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Assert.fail("There is no element for feature leaf color, but should."); |
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} |
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if (dto instanceof CategoricalDataDto){ |
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assertTrue("The states should contain one element", ((CategoricalDataDto)dto).getStates().size() == 1); |
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StateDataDto stateData = ((CategoricalDataDto)dto).getStates().iterator().next(); |
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assertEquals(uuidLeafColorBlue, stateData.getState().getUuid()); |
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}else{ |
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Assert.fail("The element is not of type categorical data"); |
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} |
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}else{ |
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Assert.fail(); |
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} |
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elements = specimen.getDataValueForFeature(uuidFeatureLeafLength); |
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if (elements != null && !elements.isEmpty() ){ |
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Iterator<DescriptionElementDto> it = elements.iterator(); |
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DescriptionElementDto dto = null; |
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if (it.hasNext()){ |
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dto = it.next(); |
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}else{ |
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Assert.fail("There is no element for feature leaf length, but should."); |
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} |
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if (dto instanceof QuantitativeDataDto){ |
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assertTrue("The statistical values should contain one element", ((QuantitativeDataDto)dto).getValues().size() == 1); |
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StatisticalMeasurementValueDto statValue = ((QuantitativeDataDto)dto).getValues().iterator().next(); |
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assertEquals(new BigDecimal("5.0"), statValue.getValue()); |
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}else{ |
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Assert.fail("The element is not of type quantitative data"); |
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} |
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}else{ |
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Assert.fail(); |
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} |
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elements = specimen.getDataValueForFeature(uuidFeatureLeafPA); |
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// assertTrue("The element should be categorical data ", element instanceof CategoricalDataDto); |
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// assertTrue("The statistical values should contain one element", ((CategoricalDataDto)element).getStates().size() == 1); |
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// StateDataDto stateData2 = ((CategoricalDataDto)element).getStates().iterator().next(); |
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// assertEquals(State.uuidPresent, stateData2.getState().getUuid()); |
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} |
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} |
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// if (row instanceof TaxonRowWrapperDTO){ |
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// TaxonRowWrapperDTO taxonRow = (TaxonRowWrapperDTO)row; |
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// Set<DescriptionElementDto> element = taxonRow.getDataValueForFeature(uuidFeatureLeafLength); |
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// assertTrue(element instanceof QuantitativeDataDto); |
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// assertTrue(((QuantitativeDataDto)element).getValues().size() == 2); |
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// } |
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} |
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commitAndStartNewTransaction(); |
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} |
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@Test |
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@DataSets({ |
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), |
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@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), |
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@DataSet(value="StructuredDescriptionAggregationTest.xml"), |
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}) |
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public void addQuantitativeDataTest() { |
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createDefaultFeatureTree(); |
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DescriptiveDataSet dataSet = createTestDataset(); |
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commitAndStartNewTransaction(); |
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List<RowWrapperDTO<?>> result = datasetService.getRowWrapper(dataSet.getUuid(), monitor); |
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List<DescriptionBaseDto> descToUpdate = new ArrayList<>(); |
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UUID updatedDescription = null; |
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int elementCount = 0; |
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for (RowWrapperDTO row: result){ |
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if (row instanceof SpecimenRowWrapperDTO){ |
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SpecimenRowWrapperDTO specimen = (SpecimenRowWrapperDTO)row; |
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DescriptionBaseDto descDto = specimen.getDescription(); |
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elementCount = descDto.getElements().size(); |
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Feature feature = (Feature)termService.find(uuidFeatureLeafLength); |
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QuantitativeDataDto quantDto = new QuantitativeDataDto(FeatureDto.fromFeature(feature)); |
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TermDto typeDto = new TermDto(StatisticalMeasure.EXACT_VALUE().getUuid(), null, StatisticalMeasure.EXACT_VALUE().getTermType(), StatisticalMeasure.EXACT_VALUE().getPartOf() != null?StatisticalMeasure.EXACT_VALUE().getPartOf().getUuid(): null, StatisticalMeasure.EXACT_VALUE().getKindOf()!= null? StatisticalMeasure.EXACT_VALUE().getKindOf().getUuid(): null, |
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StatisticalMeasure.EXACT_VALUE().getVocabulary() != null? StatisticalMeasure.EXACT_VALUE().getVocabulary().getUuid(): null, null, StatisticalMeasure.EXACT_VALUE().getIdInVocabulary(), StatisticalMeasure.EXACT_VALUE().getTitleCache()); |
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StatisticalMeasurementValueDto statValue = new StatisticalMeasurementValueDto(typeDto, new BigDecimal("4.5"), null); |
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Set<StatisticalMeasurementValueDto> values = new HashSet<>(); |
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values.add(statValue); |
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quantDto.setValues(values); |
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descDto.addElement(quantDto); |
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descToUpdate.add(descDto); |
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updatedDescription = descDto.getDescriptionUuid(); |
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} |
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} |
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descriptionService.mergeDescriptions(descToUpdate, dataSet.getUuid()); |
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commitAndStartNewTransaction(); |
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DescriptionBase description = descriptionService.load(updatedDescription); |
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assertEquals(description.getElements().size(),elementCount +1); |
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for(Object el: description.getElements()){ |
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if (el instanceof QuantitativeData){ |
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QuantitativeData descEl = (QuantitativeData)el; |
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if (descEl.getFeature().getUuid().equals(uuidFeatureLeafLength)){ |
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assertEquals(descEl.getExactValues().size(),1); |
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} |
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} |
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} |
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} |
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@Test |
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@DataSets({ |
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), |
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@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), |
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@DataSet(value="StructuredDescriptionAggregationTest.xml"), |
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}) |
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@Ignore |
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public void incompleteCategoricalDataTest() throws JvmLimitsException{ |
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createDefaultFeatureTree(); |
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DescriptiveDataSet dataSet = DescriptiveDataSet.NewInstance(); |
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datasetService.save(dataSet); |
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SpecimenDescription specDescAlpina1 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen1"); |
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addCategoricalData(specDescAlpina1, uuidFeatureLeafColor, null); |
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TaxonNode tnLapsana = taxonNodeService.find(TN_LAPSANA_UUID); |
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Assert.assertNotNull(tnLapsana); |
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dataSet.addTaxonSubtree(tnLapsana); |
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@SuppressWarnings("unchecked") |
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TermTree<Feature> descriptiveSystem = termTreeService.find(uuidFeatureTree); |
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dataSet.setDescriptiveSystem(descriptiveSystem); |
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commitAndStartNewTransaction(); |
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Taxon taxLapsanaCommunisAlpina = (Taxon)taxonService.find(T_LAPSANA_COMMUNIS_ALPINA_UUID); |
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TaxonDescription aggrDescLapsanaCommunisAlpina = testTaxonDescriptions(taxLapsanaCommunisAlpina, 1); |
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List<StateData> sdAlpinaLeafColor = testCategoricalData(uuidFeatureLeafColor, 1, aggrDescLapsanaCommunisAlpina, false); |
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testState(sdAlpinaLeafColor, uuidLeafColorBlue, 0); |
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testState(sdAlpinaLeafColor, uuidLeafColorYellow, 0); |
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} |
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private void testStatusOk(UpdateResult result) { |
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if (result.getStatus() != UpdateResult.Status.OK){ |
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Assert.fail("Aggregation should have status OK but was " + result.toString()); |
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for (Exception ex : result.getExceptions()){ |
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ex.printStackTrace(); |
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} |
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} |
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} |
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private void addLiterature(DescriptiveDataSet dataSet) { |
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//literature description |
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Taxon taxon = (Taxon)taxonService.find(T_LAPSANA_COMMUNIS_ALPINA_UUID); |
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TaxonDescription literatureDescription = TaxonDescription.NewInstance(taxon); |
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literatureDescription.addType(DescriptionType.SECONDARY_DATA); |
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addQuantitativeData(literatureDescription, uuidFeatureLeafLength, new BigDecimal("4.5"), new BigDecimal("6.5")); |
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addCategoricalData(literatureDescription, uuidFeatureLeafColor, uuidLeafColorBlue); |
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dataSet.addDescription(literatureDescription); |
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} |
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private DescriptiveDataSet createTestDataset() { |
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DescriptiveDataSet dataSet = DescriptiveDataSet.NewInstance(); |
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dataSet.setLabel("Test dataset"); |
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datasetService.save(dataSet); |
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SpecimenDescription specDescAlpina1 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen1"); |
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addCategoricalData(specDescAlpina1, uuidFeatureLeafPA, State.uuidPresent); |
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addQuantitativeData(specDescAlpina1, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("5.0")); |
|
364 |
addCategoricalData(specDescAlpina1, uuidFeatureLeafColor, uuidLeafColorBlue); |
|
365 |
|
|
366 |
SpecimenDescription specDescAlpina2 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen2"); |
|
367 |
addCategoricalData(specDescAlpina2, uuidFeatureLeafPA, State.uuidPresent); |
|
368 |
addQuantitativeData(specDescAlpina2, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("7.0")); |
|
369 |
addCategoricalData(specDescAlpina2, uuidFeatureLeafColor, uuidLeafColorBlue); |
|
370 |
|
|
371 |
SpecimenDescription specDescAlpina3 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen3"); |
|
372 |
addCategoricalData(specDescAlpina3, uuidFeatureLeafPA, State.uuidPresent); |
|
373 |
addQuantitativeData(specDescAlpina3, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("8.0")); |
|
374 |
|
|
375 |
SpecimenDescription specDescAdenophora = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ADENOPHORA_UUID, "adenophora specimen"); |
|
376 |
addCategoricalData(specDescAdenophora, uuidFeatureLeafPA, State.uuidPresent); |
|
377 |
addQuantitativeData(specDescAdenophora, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("10.0")); |
|
378 |
addCategoricalData(specDescAdenophora, uuidFeatureLeafColor, uuidLeafColorYellow); |
|
379 |
|
|
380 |
TaxonNode tnLapsana = taxonNodeService.find(TN_LAPSANA_UUID); |
|
381 |
Assert.assertNotNull(tnLapsana); |
|
382 |
dataSet.addTaxonSubtree(tnLapsana); |
|
383 |
|
|
384 |
@SuppressWarnings("unchecked") |
|
385 |
TermTree<Feature> descriptiveSystem = termTreeService.find(uuidFeatureTree); |
|
386 |
dataSet.setDescriptiveSystem(descriptiveSystem); |
|
387 |
|
|
388 |
addLiterature(dataSet); |
|
389 |
return dataSet; |
|
390 |
} |
|
391 |
|
|
392 |
private TaxonDescription testTaxonDescriptions(Taxon taxon, int elementSize){ |
|
393 |
List<TaxonDescription> taxonDescriptions = taxon.getDescriptions().stream() |
|
394 |
.filter(desc->desc.getTypes().contains(DescriptionType.AGGREGATED_STRUC_DESC)) |
|
395 |
.collect(Collectors.toList()); |
|
396 |
|
|
397 |
Assert.assertEquals(1, taxonDescriptions.size()); |
|
398 |
TaxonDescription aggrDesc = taxonDescriptions.iterator().next(); |
|
399 |
Set<DescriptionElementBase> elements = aggrDesc.getElements(); |
|
400 |
Assert.assertEquals(elementSize, elements.size()); |
|
401 |
return aggrDesc; |
|
402 |
} |
|
403 |
|
|
404 |
private void testQuantitativeData(UUID featureUuid, BigDecimal sampleSize, BigDecimal min, |
|
405 |
BigDecimal max, BigDecimal avg, TaxonDescription aggrDesc) { |
|
406 |
List<QuantitativeData> quantitativeDatas = aggrDesc.getElements().stream() |
|
407 |
.filter(element->element.getFeature().getUuid().equals(featureUuid)) |
|
408 |
.map(catData->CdmBase.deproxy(catData, QuantitativeData.class)) |
|
409 |
.collect(Collectors.toList()); |
|
410 |
Assert.assertEquals(1, quantitativeDatas.size()); |
|
411 |
QuantitativeData leafLength = quantitativeDatas.iterator().next(); |
|
412 |
Assert.assertEquals(sampleSize, leafLength.getSampleSize()); |
|
413 |
Assert.assertEquals(min, leafLength.getMin()); |
|
414 |
Assert.assertEquals(max, leafLength.getMax()); |
|
415 |
Assert.assertEquals(avg, leafLength.getAverage()); |
|
416 |
} |
|
417 |
|
|
418 |
|
|
419 |
private List<StateData> testCategoricalData(UUID featureUuid, int stateDataCount, TaxonDescription taxonDescription, boolean withAddedData) { |
|
420 |
List<CategoricalData> categoricalDatas = taxonDescription.getElements().stream() |
|
421 |
.filter(element->element.getFeature().getUuid().equals(featureUuid)) |
|
422 |
.map(catData->CdmBase.deproxy(catData, CategoricalData.class)) |
|
423 |
.collect(Collectors.toList()); |
|
424 |
int nCD = withAddedData ? 2 : 1; |
|
425 |
Assert.assertEquals(nCD, categoricalDatas.size()); |
|
426 |
CategoricalData categoricalData; |
|
427 |
if (withAddedData){ |
|
428 |
categoricalData = categoricalDatas.stream().filter(cd->cd.getStateData().get(0).getCount() != null ).findFirst().get(); |
|
429 |
}else{ |
|
430 |
categoricalData = categoricalDatas.iterator().next(); // categoricalDatas.stream().filter(cd->cd.getStateData().size() != 1).collect(Collectors.toList()); |
|
431 |
} |
|
432 |
List<StateData> stateDatas = categoricalData.getStateData(); |
|
433 |
Assert.assertEquals(stateDataCount, stateDatas.size()); |
|
434 |
return stateDatas; |
|
435 |
} |
|
436 |
|
|
437 |
private void testState(List<StateData> stateDatas, UUID stateUuid, Integer stateDataCount){ |
|
438 |
List<StateData> filteredStateDatas = stateDatas.stream() |
|
439 |
.filter(stateData->stateData.getState()!=null && stateData.getState().getUuid().equals(stateUuid)) |
|
440 |
.collect(Collectors.toList()); |
|
441 |
if(stateDataCount==0){ |
|
442 |
// non-existence test |
|
443 |
Assert.assertEquals(0, filteredStateDatas.size()); |
|
444 |
return; |
|
445 |
} |
|
446 |
Assert.assertEquals(1, filteredStateDatas.size()); |
|
447 |
StateData stateData = filteredStateDatas.iterator().next(); |
|
448 |
Assert.assertEquals(stateDataCount, stateData.getCount()); |
|
449 |
Assert.assertEquals(stateUuid, stateData.getState().getUuid()); |
|
450 |
} |
|
451 |
|
|
452 |
private void addQuantitativeData(DescriptionBase<?> desc, UUID uuidFeature, StatisticalMeasure type, BigDecimal value) { |
|
453 |
Feature feature = (Feature)termService.find(uuidFeature); |
|
454 |
QuantitativeData qd = QuantitativeData.NewInstance(feature); |
|
455 |
StatisticalMeasurementValue smv = StatisticalMeasurementValue.NewInstance(type, value); |
|
456 |
qd.addStatisticalValue(smv); |
|
457 |
desc.addElement(qd); |
|
458 |
} |
|
459 |
|
|
460 |
private void addQuantitativeData(DescriptionBase<?> desc, UUID uuidFeature, BigDecimal min, BigDecimal max) { |
|
461 |
Feature feature = (Feature)termService.find(uuidFeature); |
|
462 |
QuantitativeData qd = QuantitativeData.NewInstance(feature); |
|
463 |
StatisticalMeasurementValue smv = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min); |
|
464 |
qd.addStatisticalValue(smv); |
|
465 |
smv = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max); |
|
466 |
qd.addStatisticalValue(smv); |
|
467 |
desc.addElement(qd); |
|
468 |
} |
|
469 |
|
|
470 |
private void addCategoricalData(DescriptionBase<?> desc, UUID featureUuid, UUID stateUUID) { |
|
471 |
Feature feature = (Feature)termService.find(featureUuid); |
|
472 |
State state = (State)termService.find(stateUUID); |
|
473 |
CategoricalData cd = CategoricalData.NewInstance(state, feature); |
|
474 |
desc.addElement(cd); |
|
475 |
} |
|
476 |
|
|
477 |
private SpecimenDescription createSpecimenDescription(DescriptiveDataSet dataSet, UUID taxonUuid, String specLabel ) { |
|
478 |
Taxon taxon = (Taxon)taxonService.find(taxonUuid); |
|
479 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon); |
|
480 |
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance(); |
|
481 |
specimen.setTitleCache(specLabel, true); |
|
482 |
IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance(specimen); |
|
483 |
// TODO this has to be discussed; currently the description with the InidividualsAssociation is |
|
484 |
// needed in the dataset for performance reasons |
|
485 |
taxonDescription.addElement(individualsAssociation); |
|
486 |
dataSet.addDescription(taxonDescription); |
|
487 |
SpecimenDescription specDesc = SpecimenDescription.NewInstance(specimen); |
|
488 |
|
|
489 |
dataSet.addDescription(specDesc); |
|
490 |
return specDesc; |
|
491 |
} |
|
492 |
|
|
493 |
private Feature createFeature(UUID uuid, String label, boolean isQuantitative) { |
|
494 |
Feature feature = Feature.NewInstance("", label, null); |
|
495 |
feature.setUuid(uuid); |
|
496 |
feature.setSupportsQuantitativeData(isQuantitative); |
|
497 |
feature.setSupportsCategoricalData(!isQuantitative); |
|
498 |
feature.setSupportsTextData(false); |
|
499 |
termService.save(feature); |
|
500 |
return feature; |
|
501 |
} |
|
502 |
|
|
503 |
private State createState(String label, UUID uuid) { |
|
504 |
State state = State.NewInstance("", label, ""); |
|
505 |
state.getTitleCache(); //for better debugging |
|
506 |
state.setUuid(uuid); |
|
507 |
termService.save(state); |
|
508 |
return state; |
|
509 |
} |
|
510 |
|
|
511 |
private void createDefaultFeatureTree() { |
|
512 |
//feature tree |
|
513 |
//leaf p/a |
|
514 |
// leaf length |
|
515 |
// leaf color |
|
516 |
TermTree<Feature> featureTree = TermTree.NewFeatureInstance(); |
|
517 |
featureTree.setUuid(uuidFeatureTree); |
|
518 |
Feature featureLeafPA = createFeature(uuidFeatureLeafPA, "LeafPA", false); |
|
519 |
TermNode<Feature> leafPANode = featureTree.getRoot().addChild(featureLeafPA); |
|
520 |
Feature featureLeafLength = createFeature(uuidFeatureLeafLength, "LeafLength", true); |
|
521 |
leafPANode.addChild(featureLeafLength); |
|
522 |
Feature featureLeafColor = createFeature(uuidFeatureLeafColor, "LeafColor", false); |
|
523 |
leafPANode.addChild(featureLeafColor); |
|
524 |
State yellow = createState("Yellow", uuidLeafColorYellow); |
|
525 |
State blue = createState("Blue", uuidLeafColorBlue); |
|
526 |
TermVocabulary<State> stateVoc = TermVocabulary.NewInstance(TermType.State, State.class, "", "Colors", null, null); |
|
527 |
stateVoc.addTerm(yellow); |
|
528 |
stateVoc.addTerm(blue); |
|
529 |
featureLeafColor.addSupportedCategoricalEnumeration(stateVoc); |
|
530 |
vocabularyService.save(stateVoc); |
|
531 |
} |
|
532 |
|
|
533 |
|
|
534 |
@Override |
|
535 |
public void createTestDataSet() throws FileNotFoundException { |
|
536 |
|
|
537 |
// --- References --- // |
|
538 |
Reference sec = ReferenceFactory.newDatabase(); |
|
539 |
sec.setTitleCache("Test", true); |
|
540 |
Reference nomRef = ReferenceFactory.newBook(); |
|
541 |
sec.setTitleCache("Sp.Pl.", true); |
|
542 |
|
|
543 |
referenceService.save(sec); |
|
544 |
referenceService.save(nomRef); |
|
545 |
|
|
546 |
|
|
547 |
// --- Taxa --- // |
|
548 |
// Lapsana |
|
549 |
// L. communis |
|
550 |
// L. communis subsp. communis |
|
551 |
// L. communis subsp. adenophora |
|
552 |
// L. communis subsp. alpina |
|
553 |
// Sonchella |
|
554 |
// S. dentata |
|
555 |
// S. stenoma |
|
556 |
IBotanicalName n_lapsana = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()); |
|
557 |
n_lapsana.setTitleCache("Lapsana", true); |
|
558 |
Taxon t_lapsana = Taxon.NewInstance(n_lapsana, sec); |
|
559 |
t_lapsana.setUuid(T_LAPSANA_UUID); |
|
560 |
taxonService.saveOrUpdate(t_lapsana); |
|
561 |
|
|
562 |
IBotanicalName n_lapsana_communis = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
563 |
n_lapsana_communis.setTitleCache("L. communis", true); |
|
564 |
Taxon t_lapsana_communis = Taxon.NewInstance(n_lapsana_communis, sec); |
|
565 |
t_lapsana_communis.setUuid(T_LAPSANA_COMMUNIS_UUID); |
|
566 |
taxonService.saveOrUpdate(t_lapsana_communis); |
|
567 |
|
|
568 |
IBotanicalName n_lapsana_communis_communis = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES()); |
|
569 |
n_lapsana_communis_communis.setTitleCache("L. communis subsp. communis", true); |
|
570 |
Taxon t_lapsana_communis_communis = Taxon.NewInstance(n_lapsana_communis_communis, sec); |
|
571 |
t_lapsana_communis_communis.setUuid(T_LAPSANA_COMMUNIS_COMMUNIS_UUID); |
|
572 |
taxonService.saveOrUpdate(t_lapsana_communis_communis); |
|
573 |
|
|
574 |
IBotanicalName n_lapsana_communis_adenophora = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES()); |
|
575 |
n_lapsana_communis_adenophora.setTitleCache("L. communis subsp. adenophora", true); |
|
576 |
Taxon t_lapsana_communis_adenophora = Taxon.NewInstance(n_lapsana_communis_adenophora, sec); |
|
577 |
t_lapsana_communis_adenophora.setUuid(T_LAPSANA_COMMUNIS_ADENOPHORA_UUID); |
|
578 |
taxonService.saveOrUpdate(t_lapsana_communis_adenophora); |
|
579 |
|
|
580 |
IBotanicalName n_lapsana_communis_alpina = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES()); |
|
581 |
n_lapsana_communis_alpina.setTitleCache("L. communis subsp. alpina", true); |
|
582 |
Taxon t_lapsana_communis_alpina = Taxon.NewInstance(n_lapsana_communis_alpina, sec); |
|
583 |
t_lapsana_communis_alpina.setUuid(T_LAPSANA_COMMUNIS_ALPINA_UUID); |
|
584 |
taxonService.saveOrUpdate(t_lapsana_communis_alpina); |
|
585 |
|
|
586 |
// --- Classification --- // |
|
587 |
Classification classification = Classification.NewInstance("TestClassification"); |
|
588 |
classification.setUuid(CLASSIFICATION_UUID); |
|
589 |
classificationService.save(classification); |
|
590 |
TaxonNode node_lapsana = classification.addChildTaxon(t_lapsana, sec, null); |
|
591 |
node_lapsana.setUuid(TN_LAPSANA_UUID); |
|
592 |
TaxonNode node_lapsana_communis = node_lapsana.addChildTaxon(t_lapsana_communis, sec, null); |
|
593 |
node_lapsana_communis.addChildTaxon(t_lapsana_communis_communis, sec, null); |
|
594 |
node_lapsana_communis.addChildTaxon(t_lapsana_communis_adenophora, sec, null); |
|
595 |
node_lapsana_communis.addChildTaxon(t_lapsana_communis_alpina, sec, null); |
|
596 |
classificationService.saveOrUpdate(classification); |
|
597 |
|
|
598 |
commitAndStartNewTransaction(null); |
|
599 |
|
|
600 |
writeDbUnitDataSetFile(new String[] { |
|
601 |
"TAXONBASE", "TAXONNAME","CLASSIFICATION", "TAXONNODE","HOMOTYPICALGROUP", |
|
602 |
"REFERENCE", "AGENTBASE", |
|
603 |
"DESCRIPTIONELEMENTBASE", "DESCRIPTIONBASE", |
|
604 |
"LANGUAGESTRING", |
|
605 |
"HIBERNATE_SEQUENCES" |
|
606 |
}); |
|
607 |
} |
|
608 |
|
|
609 |
} |
cdmlib-services/src/test/java/eu/etaxonomy/cdm/api/service/description/DescriptiveDatasetServiceTest.java | ||
---|---|---|
1 |
/** |
|
2 |
* Copyright (C) 2021 EDIT |
|
3 |
* European Distributed Institute of Taxonomy |
|
4 |
* http://www.e-taxonomy.eu |
|
5 |
* |
|
6 |
* The contents of this file are subject to the Mozilla Public License Version 1.1 |
|
7 |
* See LICENSE.TXT at the top of this package for the full license terms. |
|
8 |
*/ |
|
9 |
package eu.etaxonomy.cdm.api.service.description; |
|
10 |
|
|
11 |
import static org.junit.Assert.assertEquals; |
|
12 |
import static org.junit.Assert.assertTrue; |
|
13 |
|
|
14 |
import java.io.FileNotFoundException; |
|
15 |
import java.math.BigDecimal; |
|
16 |
import java.util.ArrayList; |
|
17 |
import java.util.HashSet; |
|
18 |
import java.util.Iterator; |
|
19 |
import java.util.List; |
|
20 |
import java.util.Set; |
|
21 |
import java.util.UUID; |
|
22 |
import java.util.stream.Collectors; |
|
23 |
|
|
24 |
import org.apache.log4j.Logger; |
|
25 |
import org.junit.Assert; |
|
26 |
import org.junit.Before; |
|
27 |
import org.junit.Ignore; |
|
28 |
import org.junit.Test; |
|
29 |
import org.unitils.dbunit.annotation.DataSet; |
|
30 |
import org.unitils.dbunit.annotation.DataSets; |
|
31 |
import org.unitils.spring.annotation.SpringBeanByType; |
|
32 |
|
|
33 |
import eu.etaxonomy.cdm.api.application.ICdmRepository; |
|
34 |
import eu.etaxonomy.cdm.api.service.IClassificationService; |
|
35 |
import eu.etaxonomy.cdm.api.service.IDescriptionService; |
|
36 |
import eu.etaxonomy.cdm.api.service.IDescriptiveDataSetService; |
|
37 |
import eu.etaxonomy.cdm.api.service.IReferenceService; |
|
38 |
import eu.etaxonomy.cdm.api.service.ITaxonNodeService; |
|
39 |
import eu.etaxonomy.cdm.api.service.ITaxonService; |
|
40 |
import eu.etaxonomy.cdm.api.service.ITermService; |
|
41 |
import eu.etaxonomy.cdm.api.service.ITermTreeService; |
|
42 |
import eu.etaxonomy.cdm.api.service.IVocabularyService; |
|
43 |
import eu.etaxonomy.cdm.api.service.UpdateResult; |
|
44 |
import eu.etaxonomy.cdm.api.service.dto.CategoricalDataDto; |
|
45 |
import eu.etaxonomy.cdm.api.service.dto.DescriptionBaseDto; |
|
46 |
import eu.etaxonomy.cdm.api.service.dto.DescriptionElementDto; |
|
47 |
import eu.etaxonomy.cdm.api.service.dto.QuantitativeDataDto; |
|
48 |
import eu.etaxonomy.cdm.api.service.dto.RowWrapperDTO; |
|
49 |
import eu.etaxonomy.cdm.api.service.dto.SpecimenRowWrapperDTO; |
|
50 |
import eu.etaxonomy.cdm.api.service.dto.StateDataDto; |
|
51 |
import eu.etaxonomy.cdm.api.service.dto.StatisticalMeasurementValueDto; |
|
52 |
import eu.etaxonomy.cdm.common.JvmLimitsException; |
|
53 |
import eu.etaxonomy.cdm.common.monitor.DefaultProgressMonitor; |
|
54 |
import eu.etaxonomy.cdm.common.monitor.IProgressMonitor; |
|
55 |
import eu.etaxonomy.cdm.model.common.CdmBase; |
|
56 |
import eu.etaxonomy.cdm.model.description.CategoricalData; |
|
57 |
import eu.etaxonomy.cdm.model.description.DescriptionBase; |
|
58 |
import eu.etaxonomy.cdm.model.description.DescriptionElementBase; |
|
59 |
import eu.etaxonomy.cdm.model.description.DescriptionType; |
|
60 |
import eu.etaxonomy.cdm.model.description.DescriptiveDataSet; |
|
61 |
import eu.etaxonomy.cdm.model.description.Feature; |
|
62 |
import eu.etaxonomy.cdm.model.description.IndividualsAssociation; |
|
63 |
import eu.etaxonomy.cdm.model.description.QuantitativeData; |
|
64 |
import eu.etaxonomy.cdm.model.description.SpecimenDescription; |
|
65 |
import eu.etaxonomy.cdm.model.description.State; |
|
66 |
import eu.etaxonomy.cdm.model.description.StateData; |
|
67 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasure; |
|
68 |
import eu.etaxonomy.cdm.model.description.StatisticalMeasurementValue; |
|
69 |
import eu.etaxonomy.cdm.model.description.TaxonDescription; |
|
70 |
import eu.etaxonomy.cdm.model.name.IBotanicalName; |
|
71 |
import eu.etaxonomy.cdm.model.name.Rank; |
|
72 |
import eu.etaxonomy.cdm.model.name.TaxonNameFactory; |
|
73 |
import eu.etaxonomy.cdm.model.occurrence.DerivedUnit; |
|
74 |
import eu.etaxonomy.cdm.model.reference.Reference; |
|
75 |
import eu.etaxonomy.cdm.model.reference.ReferenceFactory; |
|
76 |
import eu.etaxonomy.cdm.model.taxon.Classification; |
|
77 |
import eu.etaxonomy.cdm.model.taxon.Taxon; |
|
78 |
import eu.etaxonomy.cdm.model.taxon.TaxonNode; |
|
79 |
import eu.etaxonomy.cdm.model.term.TermNode; |
|
80 |
import eu.etaxonomy.cdm.model.term.TermTree; |
|
81 |
import eu.etaxonomy.cdm.model.term.TermType; |
|
82 |
import eu.etaxonomy.cdm.model.term.TermVocabulary; |
|
83 |
import eu.etaxonomy.cdm.persistence.dto.FeatureDto; |
|
84 |
import eu.etaxonomy.cdm.persistence.dto.TermDto; |
|
85 |
import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest; |
|
86 |
import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy; |
|
87 |
|
|
88 |
/** |
|
89 |
* @author k.luther |
|
90 |
* @since 01.10.2021 |
|
91 |
*/ |
|
92 |
public class DescriptiveDatasetServiceTest extends CdmTransactionalIntegrationTest { |
|
93 |
|
|
94 |
@SuppressWarnings("unused") |
|
95 |
private static Logger logger = Logger.getLogger(DescriptiveDatasetServiceTest.class); |
|
96 |
|
|
97 |
|
|
98 |
private static final UUID T_LAPSANA_UUID = UUID.fromString("f65d47bd-4f49-4ab1-bc4a-bc4551eaa1a8"); |
|
99 |
private static final UUID TN_LAPSANA_UUID = UUID.fromString("f4d29e9f-6484-4184-af2e-9704e96a17e3"); |
|
100 |
|
|
101 |
private static final UUID T_LAPSANA_COMMUNIS_UUID = UUID.fromString("2a5ceebb-4830-4524-b330-78461bf8cb6b"); |
|
102 |
|
|
103 |
private static final UUID T_LAPSANA_COMMUNIS_COMMUNIS_UUID = UUID.fromString("441a3c40-0c84-11de-8c30-0800200c9a66"); |
|
104 |
|
|
105 |
private static final UUID T_LAPSANA_COMMUNIS_ADENOPHORA_UUID = UUID.fromString("e4acf200-63b6-11dd-ad8b-0800200c9a66"); |
|
106 |
|
|
107 |
private static final UUID T_LAPSANA_COMMUNIS_ALPINA_UUID = UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2"); |
|
108 |
|
|
109 |
private static final UUID CLASSIFICATION_UUID = UUID.fromString("4b266053-a841-4980-b548-3f21d8d7d712"); |
|
110 |
|
|
111 |
private static final UUID uuidFeatureLeafPA = UUID.fromString("c4dfd16f-f2ed-45e0-8f4d-7fe1ae880510"); |
|
112 |
private static UUID uuidFeatureLeafLength = UUID.fromString("3c19b50b-4a8e-467e-b7d4-89ebc05a33e1"); |
|
113 |
private static UUID uuidFeatureLeafColor = UUID.fromString("1e8f503c-5aeb-4788-b4f9-84128f7141c7"); |
|
114 |
|
|
115 |
private static UUID uuidLeafColorBlue = UUID.fromString("9b4df19d-f89d-4788-9d71-d1f6f7cae910"); |
|
116 |
private static UUID uuidLeafColorYellow = UUID.fromString("4cf0881b-0e7b-489a-9fdb-adbe6ae4e0ae"); |
|
117 |
|
|
118 |
private static UUID uuidFeatureTree = UUID.fromString("c8a29a94-2754-4d78-9faa-dff3e1387b2d"); |
|
119 |
|
|
120 |
|
|
121 |
@SpringBeanByType |
|
122 |
private ICdmRepository repository; |
|
123 |
|
|
124 |
@SpringBeanByType |
|
125 |
private ITermService termService; |
|
126 |
|
|
127 |
@SpringBeanByType |
|
128 |
private ITermTreeService termTreeService; |
|
129 |
|
|
130 |
@SpringBeanByType |
|
131 |
private IVocabularyService vocabularyService; |
|
132 |
|
|
133 |
@SpringBeanByType |
|
134 |
private IDescriptionService descriptionService; |
|
135 |
|
|
136 |
@SpringBeanByType |
|
137 |
private ITaxonService taxonService; |
|
138 |
|
|
139 |
@SpringBeanByType |
|
140 |
private ITaxonNodeService taxonNodeService; |
|
141 |
|
|
142 |
@SpringBeanByType |
|
143 |
private IClassificationService classificationService; |
|
144 |
|
|
145 |
@SpringBeanByType |
|
146 |
private IReferenceService referenceService; |
|
147 |
|
|
148 |
@SpringBeanByType |
|
149 |
private IDescriptiveDataSetService datasetService; |
|
150 |
|
|
151 |
private StructuredDescriptionAggregation engine; |
|
152 |
|
|
153 |
private IProgressMonitor monitor; |
|
154 |
|
|
155 |
@Before |
|
156 |
public void setUp() { |
|
157 |
|
|
158 |
// engine.setBatchMinFreeHeap(100 * 1024 * 1024); |
|
159 |
monitor = DefaultProgressMonitor.NewInstance(); |
|
160 |
} |
|
161 |
|
|
162 |
@Test |
|
163 |
@DataSets({ |
|
164 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), |
|
165 |
@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), |
|
166 |
@DataSet(value="StructuredDescriptionAggregationTest.xml"), |
|
167 |
}) |
|
168 |
public void testGetRowWrapper(){ |
|
169 |
createDefaultFeatureTree(); |
|
170 |
DescriptiveDataSet dataSet = createTestDataset(); |
|
171 |
commitAndStartNewTransaction(); |
|
172 |
|
|
173 |
List<RowWrapperDTO<?>> result = datasetService.getRowWrapper(dataSet.getUuid(), monitor); |
|
174 |
|
|
175 |
//There are 4 specimen descriptions and one literature description (taxon association) |
|
176 |
assertTrue(result.size() == 5); |
|
177 |
//check rowWrapper |
|
178 |
//specimen_1 2 categorical and 1 quantitative |
|
179 |
for (RowWrapperDTO row: result){ |
|
180 |
if (row instanceof SpecimenRowWrapperDTO){ |
|
181 |
SpecimenRowWrapperDTO specimen = (SpecimenRowWrapperDTO)row; |
|
182 |
if (specimen.getSpecimenDto().getLabel().equals("alpina specimen1")){ |
|
183 |
Set<DescriptionElementDto> elements = specimen.getDataValueForFeature(uuidFeatureLeafColor); |
|
184 |
if (elements != null && !elements.isEmpty() ){ |
|
185 |
Iterator<DescriptionElementDto> it = elements.iterator(); |
|
186 |
DescriptionElementDto dto = null; |
|
187 |
if (it.hasNext()){ |
|
188 |
dto = it.next(); |
|
189 |
}else{ |
|
190 |
Assert.fail("There is no element for feature leaf color, but should."); |
|
191 |
} |
|
192 |
if (dto instanceof CategoricalDataDto){ |
|
193 |
assertTrue("The states should contain one element", ((CategoricalDataDto)dto).getStates().size() == 1); |
|
194 |
StateDataDto stateData = ((CategoricalDataDto)dto).getStates().iterator().next(); |
|
195 |
assertEquals(uuidLeafColorBlue, stateData.getState().getUuid()); |
|
196 |
}else{ |
|
197 |
Assert.fail("The element is not of type categorical data"); |
|
198 |
} |
|
199 |
}else{ |
|
200 |
Assert.fail(); |
|
201 |
} |
|
202 |
|
|
203 |
|
|
204 |
elements = specimen.getDataValueForFeature(uuidFeatureLeafLength); |
|
205 |
if (elements != null && !elements.isEmpty() ){ |
|
206 |
Iterator<DescriptionElementDto> it = elements.iterator(); |
|
207 |
DescriptionElementDto dto = null; |
|
208 |
if (it.hasNext()){ |
|
209 |
dto = it.next(); |
|
210 |
}else{ |
|
211 |
Assert.fail("There is no element for feature leaf length, but should."); |
|
212 |
} |
|
213 |
if (dto instanceof QuantitativeDataDto){ |
|
214 |
assertTrue("The statistical values should contain one element", ((QuantitativeDataDto)dto).getValues().size() == 1); |
|
215 |
StatisticalMeasurementValueDto statValue = ((QuantitativeDataDto)dto).getValues().iterator().next(); |
|
216 |
assertEquals(new BigDecimal("5.0"), statValue.getValue()); |
|
217 |
}else{ |
|
218 |
Assert.fail("The element is not of type quantitative data"); |
|
219 |
} |
|
220 |
}else{ |
|
221 |
Assert.fail(); |
|
222 |
} |
|
223 |
|
|
224 |
|
|
225 |
elements = specimen.getDataValueForFeature(uuidFeatureLeafPA); |
|
226 |
// assertTrue("The element should be categorical data ", element instanceof CategoricalDataDto); |
|
227 |
// assertTrue("The statistical values should contain one element", ((CategoricalDataDto)element).getStates().size() == 1); |
|
228 |
// StateDataDto stateData2 = ((CategoricalDataDto)element).getStates().iterator().next(); |
|
229 |
// assertEquals(State.uuidPresent, stateData2.getState().getUuid()); |
|
230 |
|
|
231 |
} |
|
232 |
} |
|
233 |
// if (row instanceof TaxonRowWrapperDTO){ |
|
234 |
// TaxonRowWrapperDTO taxonRow = (TaxonRowWrapperDTO)row; |
|
235 |
// Set<DescriptionElementDto> element = taxonRow.getDataValueForFeature(uuidFeatureLeafLength); |
|
236 |
// assertTrue(element instanceof QuantitativeDataDto); |
|
237 |
// assertTrue(((QuantitativeDataDto)element).getValues().size() == 2); |
|
238 |
// } |
|
239 |
} |
|
240 |
|
|
241 |
|
|
242 |
commitAndStartNewTransaction(); |
|
243 |
|
|
244 |
} |
|
245 |
|
|
246 |
|
|
247 |
|
|
248 |
@Test |
|
249 |
@DataSets({ |
|
250 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), |
|
251 |
@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), |
|
252 |
@DataSet(value="StructuredDescriptionAggregationTest.xml"), |
|
253 |
}) |
|
254 |
public void addQuantitativeDataTest() { |
|
255 |
createDefaultFeatureTree(); |
|
256 |
DescriptiveDataSet dataSet = createTestDataset(); |
|
257 |
commitAndStartNewTransaction(); |
|
258 |
|
|
259 |
List<RowWrapperDTO<?>> result = datasetService.getRowWrapper(dataSet.getUuid(), monitor); |
|
260 |
List<DescriptionBaseDto> descToUpdate = new ArrayList<>(); |
|
261 |
UUID updatedDescription = null; |
|
262 |
int elementCount = 0; |
|
263 |
for (RowWrapperDTO row: result){ |
|
264 |
if (row instanceof SpecimenRowWrapperDTO){ |
|
265 |
SpecimenRowWrapperDTO specimen = (SpecimenRowWrapperDTO)row; |
|
266 |
DescriptionBaseDto descDto = specimen.getDescription(); |
|
267 |
elementCount = descDto.getElements().size(); |
|
268 |
Feature feature = (Feature)termService.find(uuidFeatureLeafLength); |
|
269 |
QuantitativeDataDto quantDto = new QuantitativeDataDto(FeatureDto.fromFeature(feature)); |
|
270 |
TermDto typeDto = new TermDto(StatisticalMeasure.EXACT_VALUE().getUuid(), null, StatisticalMeasure.EXACT_VALUE().getTermType(), StatisticalMeasure.EXACT_VALUE().getPartOf() != null?StatisticalMeasure.EXACT_VALUE().getPartOf().getUuid(): null, StatisticalMeasure.EXACT_VALUE().getKindOf()!= null? StatisticalMeasure.EXACT_VALUE().getKindOf().getUuid(): null, |
|
271 |
StatisticalMeasure.EXACT_VALUE().getVocabulary() != null? StatisticalMeasure.EXACT_VALUE().getVocabulary().getUuid(): null, null, StatisticalMeasure.EXACT_VALUE().getIdInVocabulary(), StatisticalMeasure.EXACT_VALUE().getTitleCache()); |
|
272 |
StatisticalMeasurementValueDto statValue = new StatisticalMeasurementValueDto(typeDto, new BigDecimal("4.5"), null); |
|
273 |
Set<StatisticalMeasurementValueDto> values = new HashSet<>(); |
|
274 |
values.add(statValue); |
|
275 |
quantDto.setValues(values); |
|
276 |
descDto.addElement(quantDto); |
|
277 |
descToUpdate.add(descDto); |
|
278 |
updatedDescription = descDto.getDescriptionUuid(); |
|
279 |
|
|
280 |
} |
|
281 |
} |
|
282 |
descriptionService.mergeDescriptions(descToUpdate, dataSet.getUuid()); |
|
283 |
|
|
284 |
commitAndStartNewTransaction(); |
|
285 |
DescriptionBase description = descriptionService.load(updatedDescription); |
|
286 |
assertEquals(description.getElements().size(),elementCount +1); |
|
287 |
for(Object el: description.getElements()){ |
|
288 |
if (el instanceof QuantitativeData){ |
|
289 |
QuantitativeData descEl = (QuantitativeData)el; |
|
290 |
if (descEl.getFeature().getUuid().equals(uuidFeatureLeafLength)){ |
|
291 |
assertEquals(descEl.getExactValues().size(),1); |
|
292 |
} |
|
293 |
} |
|
294 |
} |
|
295 |
|
|
296 |
} |
|
297 |
|
|
298 |
@Test |
|
299 |
@DataSets({ |
|
300 |
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"), |
|
301 |
@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"), |
|
302 |
@DataSet(value="StructuredDescriptionAggregationTest.xml"), |
|
303 |
}) |
|
304 |
@Ignore |
|
305 |
public void incompleteCategoricalDataTest() throws JvmLimitsException{ |
|
306 |
createDefaultFeatureTree(); |
|
307 |
DescriptiveDataSet dataSet = DescriptiveDataSet.NewInstance(); |
|
308 |
datasetService.save(dataSet); |
|
309 |
|
|
310 |
SpecimenDescription specDescAlpina1 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen1"); |
|
311 |
addCategoricalData(specDescAlpina1, uuidFeatureLeafColor, null); |
|
312 |
|
|
313 |
TaxonNode tnLapsana = taxonNodeService.find(TN_LAPSANA_UUID); |
|
314 |
Assert.assertNotNull(tnLapsana); |
|
315 |
dataSet.addTaxonSubtree(tnLapsana); |
|
316 |
|
|
317 |
@SuppressWarnings("unchecked") |
|
318 |
TermTree<Feature> descriptiveSystem = termTreeService.find(uuidFeatureTree); |
|
319 |
dataSet.setDescriptiveSystem(descriptiveSystem); |
|
320 |
commitAndStartNewTransaction(); |
|
321 |
|
|
322 |
|
|
323 |
|
|
324 |
Taxon taxLapsanaCommunisAlpina = (Taxon)taxonService.find(T_LAPSANA_COMMUNIS_ALPINA_UUID); |
|
325 |
TaxonDescription aggrDescLapsanaCommunisAlpina = testTaxonDescriptions(taxLapsanaCommunisAlpina, 1); |
|
326 |
List<StateData> sdAlpinaLeafColor = testCategoricalData(uuidFeatureLeafColor, 1, aggrDescLapsanaCommunisAlpina, false); |
|
327 |
testState(sdAlpinaLeafColor, uuidLeafColorBlue, 0); |
|
328 |
testState(sdAlpinaLeafColor, uuidLeafColorYellow, 0); |
|
329 |
} |
|
330 |
|
|
331 |
|
|
332 |
private void testStatusOk(UpdateResult result) { |
|
333 |
if (result.getStatus() != UpdateResult.Status.OK){ |
|
334 |
Assert.fail("Aggregation should have status OK but was " + result.toString()); |
|
335 |
for (Exception ex : result.getExceptions()){ |
|
336 |
ex.printStackTrace(); |
|
337 |
} |
|
338 |
} |
|
339 |
} |
|
340 |
|
|
341 |
private void addLiterature(DescriptiveDataSet dataSet) { |
|
342 |
|
|
343 |
//literature description |
|
344 |
Taxon taxon = (Taxon)taxonService.find(T_LAPSANA_COMMUNIS_ALPINA_UUID); |
|
345 |
TaxonDescription literatureDescription = TaxonDescription.NewInstance(taxon); |
|
346 |
literatureDescription.addType(DescriptionType.SECONDARY_DATA); |
|
347 |
addQuantitativeData(literatureDescription, uuidFeatureLeafLength, new BigDecimal("4.5"), new BigDecimal("6.5")); |
|
348 |
addCategoricalData(literatureDescription, uuidFeatureLeafColor, uuidLeafColorBlue); |
|
349 |
dataSet.addDescription(literatureDescription); |
|
350 |
} |
|
351 |
|
|
352 |
|
|
353 |
|
|
354 |
|
|
355 |
|
|
356 |
private DescriptiveDataSet createTestDataset() { |
|
357 |
DescriptiveDataSet dataSet = DescriptiveDataSet.NewInstance(); |
|
358 |
dataSet.setLabel("Test dataset"); |
|
359 |
datasetService.save(dataSet); |
|
360 |
|
|
361 |
SpecimenDescription specDescAlpina1 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen1"); |
|
362 |
addCategoricalData(specDescAlpina1, uuidFeatureLeafPA, State.uuidPresent); |
|
363 |
addQuantitativeData(specDescAlpina1, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("5.0")); |
|
364 |
addCategoricalData(specDescAlpina1, uuidFeatureLeafColor, uuidLeafColorBlue); |
|
365 |
|
|
366 |
SpecimenDescription specDescAlpina2 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen2"); |
|
367 |
addCategoricalData(specDescAlpina2, uuidFeatureLeafPA, State.uuidPresent); |
|
368 |
addQuantitativeData(specDescAlpina2, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("7.0")); |
|
369 |
addCategoricalData(specDescAlpina2, uuidFeatureLeafColor, uuidLeafColorBlue); |
|
370 |
|
|
371 |
SpecimenDescription specDescAlpina3 = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ALPINA_UUID, "alpina specimen3"); |
|
372 |
addCategoricalData(specDescAlpina3, uuidFeatureLeafPA, State.uuidPresent); |
|
373 |
addQuantitativeData(specDescAlpina3, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("8.0")); |
|
374 |
|
|
375 |
SpecimenDescription specDescAdenophora = createSpecimenDescription(dataSet, T_LAPSANA_COMMUNIS_ADENOPHORA_UUID, "adenophora specimen"); |
|
376 |
addCategoricalData(specDescAdenophora, uuidFeatureLeafPA, State.uuidPresent); |
|
377 |
addQuantitativeData(specDescAdenophora, uuidFeatureLeafLength, StatisticalMeasure.EXACT_VALUE(), new BigDecimal("10.0")); |
|
378 |
addCategoricalData(specDescAdenophora, uuidFeatureLeafColor, uuidLeafColorYellow); |
|
379 |
|
|
380 |
TaxonNode tnLapsana = taxonNodeService.find(TN_LAPSANA_UUID); |
|
381 |
Assert.assertNotNull(tnLapsana); |
|
382 |
dataSet.addTaxonSubtree(tnLapsana); |
|
383 |
|
|
384 |
@SuppressWarnings("unchecked") |
|
385 |
TermTree<Feature> descriptiveSystem = termTreeService.find(uuidFeatureTree); |
|
386 |
dataSet.setDescriptiveSystem(descriptiveSystem); |
|
387 |
|
|
388 |
addLiterature(dataSet); |
|
389 |
return dataSet; |
|
390 |
} |
|
391 |
|
|
392 |
private TaxonDescription testTaxonDescriptions(Taxon taxon, int elementSize){ |
|
393 |
List<TaxonDescription> taxonDescriptions = taxon.getDescriptions().stream() |
|
394 |
.filter(desc->desc.getTypes().contains(DescriptionType.AGGREGATED_STRUC_DESC)) |
|
395 |
.collect(Collectors.toList()); |
|
396 |
|
|
397 |
Assert.assertEquals(1, taxonDescriptions.size()); |
|
398 |
TaxonDescription aggrDesc = taxonDescriptions.iterator().next(); |
|
399 |
Set<DescriptionElementBase> elements = aggrDesc.getElements(); |
|
400 |
Assert.assertEquals(elementSize, elements.size()); |
|
401 |
return aggrDesc; |
|
402 |
} |
|
403 |
|
|
404 |
private void testQuantitativeData(UUID featureUuid, BigDecimal sampleSize, BigDecimal min, |
|
405 |
BigDecimal max, BigDecimal avg, TaxonDescription aggrDesc) { |
|
406 |
List<QuantitativeData> quantitativeDatas = aggrDesc.getElements().stream() |
|
407 |
.filter(element->element.getFeature().getUuid().equals(featureUuid)) |
|
408 |
.map(catData->CdmBase.deproxy(catData, QuantitativeData.class)) |
|
409 |
.collect(Collectors.toList()); |
|
410 |
Assert.assertEquals(1, quantitativeDatas.size()); |
|
411 |
QuantitativeData leafLength = quantitativeDatas.iterator().next(); |
|
412 |
Assert.assertEquals(sampleSize, leafLength.getSampleSize()); |
|
413 |
Assert.assertEquals(min, leafLength.getMin()); |
|
414 |
Assert.assertEquals(max, leafLength.getMax()); |
|
415 |
Assert.assertEquals(avg, leafLength.getAverage()); |
|
416 |
} |
|
417 |
|
|
418 |
|
|
419 |
private List<StateData> testCategoricalData(UUID featureUuid, int stateDataCount, TaxonDescription taxonDescription, boolean withAddedData) { |
|
420 |
List<CategoricalData> categoricalDatas = taxonDescription.getElements().stream() |
|
421 |
.filter(element->element.getFeature().getUuid().equals(featureUuid)) |
|
422 |
.map(catData->CdmBase.deproxy(catData, CategoricalData.class)) |
|
423 |
.collect(Collectors.toList()); |
|
424 |
int nCD = withAddedData ? 2 : 1; |
|
425 |
Assert.assertEquals(nCD, categoricalDatas.size()); |
|
426 |
CategoricalData categoricalData; |
|
427 |
if (withAddedData){ |
|
428 |
categoricalData = categoricalDatas.stream().filter(cd->cd.getStateData().get(0).getCount() != null ).findFirst().get(); |
|
429 |
}else{ |
|
430 |
categoricalData = categoricalDatas.iterator().next(); // categoricalDatas.stream().filter(cd->cd.getStateData().size() != 1).collect(Collectors.toList()); |
|
431 |
} |
|
432 |
List<StateData> stateDatas = categoricalData.getStateData(); |
|
433 |
Assert.assertEquals(stateDataCount, stateDatas.size()); |
|
434 |
return stateDatas; |
|
435 |
} |
|
436 |
|
|
437 |
private void testState(List<StateData> stateDatas, UUID stateUuid, Integer stateDataCount){ |
|
438 |
List<StateData> filteredStateDatas = stateDatas.stream() |
|
439 |
.filter(stateData->stateData.getState()!=null && stateData.getState().getUuid().equals(stateUuid)) |
|
440 |
.collect(Collectors.toList()); |
|
441 |
if(stateDataCount==0){ |
|
442 |
// non-existence test |
|
443 |
Assert.assertEquals(0, filteredStateDatas.size()); |
|
444 |
return; |
|
445 |
} |
|
446 |
Assert.assertEquals(1, filteredStateDatas.size()); |
|
447 |
StateData stateData = filteredStateDatas.iterator().next(); |
|
448 |
Assert.assertEquals(stateDataCount, stateData.getCount()); |
|
449 |
Assert.assertEquals(stateUuid, stateData.getState().getUuid()); |
|
450 |
} |
|
451 |
|
|
452 |
private void addQuantitativeData(DescriptionBase<?> desc, UUID uuidFeature, StatisticalMeasure type, BigDecimal value) { |
|
453 |
Feature feature = (Feature)termService.find(uuidFeature); |
|
454 |
QuantitativeData qd = QuantitativeData.NewInstance(feature); |
|
455 |
StatisticalMeasurementValue smv = StatisticalMeasurementValue.NewInstance(type, value); |
|
456 |
qd.addStatisticalValue(smv); |
|
457 |
desc.addElement(qd); |
|
458 |
} |
|
459 |
|
|
460 |
private void addQuantitativeData(DescriptionBase<?> desc, UUID uuidFeature, BigDecimal min, BigDecimal max) { |
|
461 |
Feature feature = (Feature)termService.find(uuidFeature); |
|
462 |
QuantitativeData qd = QuantitativeData.NewInstance(feature); |
|
463 |
StatisticalMeasurementValue smv = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MIN(), min); |
|
464 |
qd.addStatisticalValue(smv); |
|
465 |
smv = StatisticalMeasurementValue.NewInstance(StatisticalMeasure.MAX(), max); |
|
466 |
qd.addStatisticalValue(smv); |
|
467 |
desc.addElement(qd); |
|
468 |
} |
|
469 |
|
|
470 |
private void addCategoricalData(DescriptionBase<?> desc, UUID featureUuid, UUID stateUUID) { |
|
471 |
Feature feature = (Feature)termService.find(featureUuid); |
|
472 |
State state = (State)termService.find(stateUUID); |
|
473 |
CategoricalData cd = CategoricalData.NewInstance(state, feature); |
|
474 |
desc.addElement(cd); |
|
475 |
} |
|
476 |
|
|
477 |
private SpecimenDescription createSpecimenDescription(DescriptiveDataSet dataSet, UUID taxonUuid, String specLabel ) { |
|
478 |
Taxon taxon = (Taxon)taxonService.find(taxonUuid); |
|
479 |
TaxonDescription taxonDescription = TaxonDescription.NewInstance(taxon); |
|
480 |
DerivedUnit specimen = DerivedUnit.NewPreservedSpecimenInstance(); |
|
481 |
specimen.setTitleCache(specLabel, true); |
|
482 |
IndividualsAssociation individualsAssociation = IndividualsAssociation.NewInstance(specimen); |
|
483 |
// TODO this has to be discussed; currently the description with the InidividualsAssociation is |
|
484 |
// needed in the dataset for performance reasons |
|
485 |
taxonDescription.addElement(individualsAssociation); |
|
486 |
dataSet.addDescription(taxonDescription); |
|
487 |
SpecimenDescription specDesc = SpecimenDescription.NewInstance(specimen); |
|
488 |
|
|
489 |
dataSet.addDescription(specDesc); |
|
490 |
return specDesc; |
|
491 |
} |
|
492 |
|
|
493 |
private Feature createFeature(UUID uuid, String label, boolean isQuantitative) { |
|
494 |
Feature feature = Feature.NewInstance("", label, null); |
|
495 |
feature.setUuid(uuid); |
|
496 |
feature.setSupportsQuantitativeData(isQuantitative); |
|
497 |
feature.setSupportsCategoricalData(!isQuantitative); |
|
498 |
feature.setSupportsTextData(false); |
|
499 |
termService.save(feature); |
|
500 |
return feature; |
|
501 |
} |
|
502 |
|
|
503 |
private State createState(String label, UUID uuid) { |
|
504 |
State state = State.NewInstance("", label, ""); |
|
505 |
state.getTitleCache(); //for better debugging |
|
506 |
state.setUuid(uuid); |
|
507 |
termService.save(state); |
|
508 |
return state; |
|
509 |
} |
|
510 |
|
|
511 |
private void createDefaultFeatureTree() { |
|
512 |
//feature tree |
|
513 |
//leaf p/a |
|
514 |
// leaf length |
|
515 |
// leaf color |
|
516 |
TermTree<Feature> featureTree = TermTree.NewFeatureInstance(); |
|
517 |
featureTree.setUuid(uuidFeatureTree); |
|
518 |
Feature featureLeafPA = createFeature(uuidFeatureLeafPA, "LeafPA", false); |
|
519 |
TermNode<Feature> leafPANode = featureTree.getRoot().addChild(featureLeafPA); |
|
520 |
Feature featureLeafLength = createFeature(uuidFeatureLeafLength, "LeafLength", true); |
|
521 |
leafPANode.addChild(featureLeafLength); |
|
522 |
Feature featureLeafColor = createFeature(uuidFeatureLeafColor, "LeafColor", false); |
|
523 |
leafPANode.addChild(featureLeafColor); |
|
524 |
State yellow = createState("Yellow", uuidLeafColorYellow); |
|
525 |
State blue = createState("Blue", uuidLeafColorBlue); |
|
526 |
TermVocabulary<State> stateVoc = TermVocabulary.NewInstance(TermType.State, State.class, "", "Colors", null, null); |
|
527 |
stateVoc.addTerm(yellow); |
|
528 |
stateVoc.addTerm(blue); |
|
529 |
featureLeafColor.addSupportedCategoricalEnumeration(stateVoc); |
|
530 |
vocabularyService.save(stateVoc); |
|
531 |
} |
|
532 |
|
|
533 |
|
|
534 |
@Override |
|
535 |
public void createTestDataSet() throws FileNotFoundException { |
|
536 |
|
|
537 |
// --- References --- // |
|
538 |
Reference sec = ReferenceFactory.newDatabase(); |
|
539 |
sec.setTitleCache("Test", true); |
|
540 |
Reference nomRef = ReferenceFactory.newBook(); |
|
541 |
sec.setTitleCache("Sp.Pl.", true); |
|
542 |
|
|
543 |
referenceService.save(sec); |
|
544 |
referenceService.save(nomRef); |
|
545 |
|
|
546 |
|
|
547 |
// --- Taxa --- // |
|
548 |
// Lapsana |
|
549 |
// L. communis |
|
550 |
// L. communis subsp. communis |
|
551 |
// L. communis subsp. adenophora |
|
552 |
// L. communis subsp. alpina |
|
553 |
// Sonchella |
|
554 |
// S. dentata |
|
555 |
// S. stenoma |
|
556 |
IBotanicalName n_lapsana = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS()); |
|
557 |
n_lapsana.setTitleCache("Lapsana", true); |
|
558 |
Taxon t_lapsana = Taxon.NewInstance(n_lapsana, sec); |
|
559 |
t_lapsana.setUuid(T_LAPSANA_UUID); |
|
560 |
taxonService.saveOrUpdate(t_lapsana); |
|
561 |
|
|
562 |
IBotanicalName n_lapsana_communis = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES()); |
|
563 |
n_lapsana_communis.setTitleCache("L. communis", true); |
|
564 |
Taxon t_lapsana_communis = Taxon.NewInstance(n_lapsana_communis, sec); |
|
565 |
t_lapsana_communis.setUuid(T_LAPSANA_COMMUNIS_UUID); |
|
566 |
taxonService.saveOrUpdate(t_lapsana_communis); |
|
567 |
|
|
568 |
IBotanicalName n_lapsana_communis_communis = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES()); |
|
569 |
n_lapsana_communis_communis.setTitleCache("L. communis subsp. communis", true); |
|
570 |
Taxon t_lapsana_communis_communis = Taxon.NewInstance(n_lapsana_communis_communis, sec); |
|
571 |
t_lapsana_communis_communis.setUuid(T_LAPSANA_COMMUNIS_COMMUNIS_UUID); |
|
572 |
taxonService.saveOrUpdate(t_lapsana_communis_communis); |
|
573 |
|
|
574 |
IBotanicalName n_lapsana_communis_adenophora = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES()); |
|
575 |
n_lapsana_communis_adenophora.setTitleCache("L. communis subsp. adenophora", true); |
|
576 |
Taxon t_lapsana_communis_adenophora = Taxon.NewInstance(n_lapsana_communis_adenophora, sec); |
|
577 |
t_lapsana_communis_adenophora.setUuid(T_LAPSANA_COMMUNIS_ADENOPHORA_UUID); |
|
578 |
taxonService.saveOrUpdate(t_lapsana_communis_adenophora); |
|
579 |
|
|
580 |
IBotanicalName n_lapsana_communis_alpina = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES()); |
|
581 |
n_lapsana_communis_alpina.setTitleCache("L. communis subsp. alpina", true); |
|
582 |
Taxon t_lapsana_communis_alpina = Taxon.NewInstance(n_lapsana_communis_alpina, sec); |
|
583 |
t_lapsana_communis_alpina.setUuid(T_LAPSANA_COMMUNIS_ALPINA_UUID); |
|
584 |
taxonService.saveOrUpdate(t_lapsana_communis_alpina); |
|
585 |
|
|
586 |
// --- Classification --- // |
|
587 |
Classification classification = Classification.NewInstance("TestClassification"); |
|
588 |
classification.setUuid(CLASSIFICATION_UUID); |
|
589 |
classificationService.save(classification); |
|
590 |
TaxonNode node_lapsana = classification.addChildTaxon(t_lapsana, sec, null); |
|
591 |
node_lapsana.setUuid(TN_LAPSANA_UUID); |
|
592 |
TaxonNode node_lapsana_communis = node_lapsana.addChildTaxon(t_lapsana_communis, sec, null); |
|
593 |
node_lapsana_communis.addChildTaxon(t_lapsana_communis_communis, sec, null); |
|
594 |
node_lapsana_communis.addChildTaxon(t_lapsana_communis_adenophora, sec, null); |
|
595 |
node_lapsana_communis.addChildTaxon(t_lapsana_communis_alpina, sec, null); |
|
596 |
classificationService.saveOrUpdate(classification); |
|
597 |
|
|
598 |
commitAndStartNewTransaction(null); |
|
599 |
|
|
600 |
writeDbUnitDataSetFile(new String[] { |
|
601 |
"TAXONBASE", "TAXONNAME","CLASSIFICATION", "TAXONNODE","HOMOTYPICALGROUP", |
|
602 |
"REFERENCE", "AGENTBASE", |
|
603 |
"DESCRIPTIONELEMENTBASE", "DESCRIPTIONBASE", |
|
604 |
"LANGUAGESTRING", |
|
605 |
"HIBERNATE_SEQUENCES" |
|
606 |
}); |
|
607 |
} |
|
608 |
|
|
609 |
} |
Also available in: Unified diff
rename DescriptiveDataSetServiceTest