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/**
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* Copyright (C) 2013 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.assertNotNull;
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import static org.junit.Assert.assertNull;
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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.Arrays;
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import java.util.Collection;
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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 org.apache.log4j.Logger;
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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.service.IClassificationService;
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import eu.etaxonomy.cdm.api.service.IReferenceService;
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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.description.TransmissionEngineDistribution;
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import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution.AggregationMode;
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import eu.etaxonomy.cdm.common.JvmLimitsException;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
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import eu.etaxonomy.cdm.model.description.Distribution;
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import eu.etaxonomy.cdm.model.description.PresenceAbsenceTerm;
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import eu.etaxonomy.cdm.model.description.TaxonDescription;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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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.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.test.integration.CdmTransactionalIntegrationTest;
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import eu.etaxonomy.cdm.test.unitils.CleanSweepInsertLoadStrategy;
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/**
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* @author a.kohlbecker
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* @since Feb 26, 2013
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*
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*/
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public class TransmissionEngineDistributionTest extends CdmTransactionalIntegrationTest {
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private static Logger logger = Logger.getLogger(TransmissionEngineDistributionTest.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 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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@SpringBeanByType
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private ITermService termService;
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@SpringBeanByType
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private ITaxonService taxonService;
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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 TransmissionEngineDistribution engine;
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// --- Distributions --- //
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// tdwg3 level YUG : Yugoslavia
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// contains tdwg4 level areas :
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// YUG-BH Bosnia-Herzegovina
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// YUG-CR Croatia
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// YUG-KO Kosovo
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// YUG-MA Macedonia
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// YUG-MN Montenegro
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private NamedArea yug = null;
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private NamedArea yug_bh = null;
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private NamedArea yug_cr = null;
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private NamedArea yug_ko = null;
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private NamedArea yug_ma = null;
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private NamedArea yug_mn = null;
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List<NamedArea> superAreas = null;
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Rank upperRank = null;
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Rank lowerRank = null;
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private Classification classification;
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private Reference book_a = null;
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private Reference book_b = null;
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@Before
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public void setUp() {
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superAreas = Arrays.asList(new NamedArea[]{
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termService.getAreaByTdwgAbbreviation("YUG")
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});
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lowerRank = Rank.SUBSPECIES();
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upperRank = Rank.GENUS();
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classification = classificationService.load(CLASSIFICATION_UUID);
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yug = termService.getAreaByTdwgAbbreviation("YUG");
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yug_bh = termService.getAreaByTdwgAbbreviation("YUG-BH");
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yug_cr = termService.getAreaByTdwgAbbreviation("YUG-CR");
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yug_ko = termService.getAreaByTdwgAbbreviation("YUG-KO");
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yug_ma = termService.getAreaByTdwgAbbreviation("YUG-MA");
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yug_mn = termService.getAreaByTdwgAbbreviation("YUG-MN");
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book_a = ReferenceFactory.newBook();
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book_a.setTitle("book_a");
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book_b = ReferenceFactory.newBook();
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book_b.setTitle("book_a");
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engine.setBatchMinFreeHeap(100 * 1024 * 1024);
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engine.updatePriorities();
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}
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@Test
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@DataSet
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public void testPriorities(){
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Set<Extension> extensions = termService.load(PresenceAbsenceTerm.CULTIVATED().getUuid()).getExtensions();
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assertEquals(TransmissionEngineDistribution.EXTENSION_VALUE_PREFIX + "45", extensions.iterator().next().getValue());
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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="TransmissionEngineDistributionTest.xml"),
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})
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// @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class) //, value="./ClearDBDataSet.xml")
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public void test_ignore() throws JvmLimitsException {
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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Arrays.asList(new Distribution[] {
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// should succeed during area aggregation be ignored by rank aggregation
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// => yug will get status ENDEMIC_FOR_THE_RELEVANT_AREA
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// but only for LAPSANA_COMMUNIS_ALPINA
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Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA()),
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// should be ignored by area aggregation
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// => LAPSANA_COMMUNIS will wave distribution with yug_ko and INTRODUCED_FORMERLY_INTRODUCED
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Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED()),
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})
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);
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engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);
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Taxon lapsana_communis_alpina = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_ALPINA_UUID);
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assertEquals(2, lapsana_communis_alpina.getDescriptions().size());
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// TODO test for yug => ENDEMIC_FOR_THE_RELEVANT_AREA in computed description
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Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);
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assertEquals(1, lapsana_communis.getDescriptions().size());
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TaxonDescription description = lapsana_communis.getDescriptions().iterator().next();
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assertEquals(1, description.getElements().size());
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int numExpectedFound = 0;
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for (DescriptionElementBase element : description.getElements()){
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Distribution distribution = (Distribution)element;
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if(distribution.getArea().equals(yug_ko)){
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numExpectedFound++;
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assertEquals("aggregated status of area YUG-KO wrong", PresenceAbsenceTerm.INTRODUCED_FORMERLY_INTRODUCED().getLabel(), distribution.getStatus().getLabel());
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}
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}
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assertEquals("All three expected areas should have been found before", numExpectedFound, 1);
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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="TransmissionEngineDistributionTest.xml"),
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})
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public void testArea_area() throws JvmLimitsException {
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Set<Distribution> distributions_LCA = new HashSet<>();
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distributions_LCA.add(newDistribution(book_a, yug_mn, PresenceAbsenceTerm.CULTIVATED(), "1"));
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distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "2")); // NATIVE should succeed
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distributions_LCA.add(newDistribution(book_a, yug_bh, PresenceAbsenceTerm.INTRODUCED(), "3"));
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distributions_LCA.add(newDistribution(book_a, yug_ma, PresenceAbsenceTerm.NATIVE(), "4")); // NATIVE should succeed
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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distributions_LCA
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);
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Taxon lapsana_communis_alpina = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_ALPINA_UUID);
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assertEquals(1, lapsana_communis_alpina.getDescriptions().size());
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engine.accumulate(AggregationMode.byAreas, superAreas, lowerRank, upperRank, classification, null);
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lapsana_communis_alpina = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_ALPINA_UUID);
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assertEquals(2, lapsana_communis_alpina.getDescriptions().size());
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Distribution accumulatedDistribution = null;
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for (TaxonDescription description : lapsana_communis_alpina.getDescriptions()) {
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if(description.hasMarker(MarkerType.COMPUTED(), true)) {
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assertNull("only one computed Distribution should exists", accumulatedDistribution);
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assertEquals("the computed Decsription should have only one element", 1, description.getElements().size());
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accumulatedDistribution = (Distribution) description.getElements().iterator().next();
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assertEquals("Expecting area to be YUG", yug, accumulatedDistribution.getArea());
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assertEquals("Expecting status to be NATIVE", PresenceAbsenceTerm.NATIVE().getLabel(), accumulatedDistribution.getStatus().getLabel());
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}
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}
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assertNotNull("The area YUG should have been found", accumulatedDistribution);
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assertEquals("Expecting two source references", 2, accumulatedDistribution.getSources().size());
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Iterator<DescriptionElementSource> sourceIt = accumulatedDistribution.getSources().iterator();
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// should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests
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assertTrue(" 2 4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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assertTrue(" 2 4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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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="TransmissionEngineDistributionTest.xml"),
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})
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public void testArea_rank_and_area_1() throws JvmLimitsException {
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Set<Distribution> distributions_LCA = new HashSet<>();
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distributions_LCA.add(newDistribution(book_a, yug_mn, PresenceAbsenceTerm.CULTIVATED(), "1"));
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distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "2")); // NATIVE should succeed
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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distributions_LCA
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);
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Set<Distribution> distributions_LC = new HashSet<>();
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distributions_LC.add(newDistribution(book_a, yug_mn, PresenceAbsenceTerm.CULTIVATED(), "3"));
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distributions_LC.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "4")); // NATIVE should succeed
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commitAndStartNewTransaction(null);
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addDistributions(
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T_LAPSANA_COMMUNIS_UUID,
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distributions_LC
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);
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engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);
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Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);
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assertEquals("Lapsana communis alpina must only have 2 Descriptions", 2, lapsana_communis.getDescriptions().size());
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Taxon lapsana = (Taxon) taxonService.load(T_LAPSANA_UUID);
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assertEquals("Lapsana communis must only have 1 Description", 1, lapsana.getDescriptions().size());
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TaxonDescription description = lapsana.getDescriptions().iterator().next();
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assertTrue(description.hasMarker(MarkerType.COMPUTED(), true));
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assertEquals(3, description.getElements().size());
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int numExpectedFound = 0;
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for (DescriptionElementBase element : description.getElements()){
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Distribution distribution = (Distribution)element;
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if(distribution.getArea().equals(yug)){
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numExpectedFound++;
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assertEquals("aggregated status of area YUG is wrong", PresenceAbsenceTerm.NATIVE().getLabel(), distribution.getStatus().getLabel());
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assertEquals(2, distribution.getSources().size());
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Iterator<DescriptionElementSource> sourceIt = distribution.getSources().iterator();
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// should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests
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assertTrue(" 2 4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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assertTrue(" 2 4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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}
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if(distribution.getArea().equals(yug_mn)){
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numExpectedFound++;
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assertEquals("aggregated status of area YUG-MN is wrong", PresenceAbsenceTerm.CULTIVATED().getLabel(), distribution.getStatus().getLabel());
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assertEquals(2, distribution.getSources().size());
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Iterator<DescriptionElementSource> sourceIt = distribution.getSources().iterator();
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// should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests
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assertTrue(" 1 3 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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assertTrue(" 1 3 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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}
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if(distribution.getArea().equals(yug_ko)){
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numExpectedFound++;
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assertEquals("aggregated status of area YUG-KO wrong", PresenceAbsenceTerm.NATIVE().getLabel(), distribution.getStatus().getLabel());
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assertEquals(2, distribution.getSources().size());
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Iterator<DescriptionElementSource> sourceIt = distribution.getSources().iterator();
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// should contain source_LCA_yug_ma and source_LCA_yug_ko, testing the microreference which is unique in the tests
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assertTrue(" 2 4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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assertTrue(" 2 4 ".contains(" " + sourceIt.next().getCitationMicroReference() + " "));
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}
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}
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assertEquals("All three expected areas should have been found before", numExpectedFound, 3);
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}
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/**
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* Variant of {@link #testArea_rank_and_area_1()} with alternate source references to check the
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* suppression of duplicates.
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*
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* This test relies on {@link #testArea_rank_and_area_1()}
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* an makes assertions only on the alternative source references
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* @throws JvmLimitsException
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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="TransmissionEngineDistributionTest.xml"),
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})
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public void testArea_rank_and_area_2() throws JvmLimitsException {
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Set<Distribution> distributions_LCA = new HashSet<Distribution>();
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distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));
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distributions_LCA.add(newDistribution(book_b, yug_ko, PresenceAbsenceTerm.NATIVE(), "2"));
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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distributions_LCA
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);
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engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);
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Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);
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int computedDescriptionsCnt = 0;
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for(TaxonDescription description : lapsana_communis.getDescriptions()) {
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if(description.hasMarker(MarkerType.COMPUTED(), true)) {
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computedDescriptionsCnt++;
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349
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assertEquals(2, description.getElements().size()); // yug, yug_ko
|
350
|
for(DescriptionElementBase distribution : description.getElements()) {
|
351
|
logger.debug(((Distribution)distribution).getArea() + " " + sourcesToString(distribution));
|
352
|
if(((Distribution)distribution).getArea().equals(yug_ko)){
|
353
|
assertEquals(2, distribution.getSources().size());
|
354
|
}
|
355
|
if(((Distribution)distribution).getArea().equals(yug)){
|
356
|
assertEquals(2, distribution.getSources().size());
|
357
|
}
|
358
|
}
|
359
|
}
|
360
|
}
|
361
|
assertEquals(1, computedDescriptionsCnt);
|
362
|
}
|
363
|
|
364
|
|
365
|
/**
|
366
|
* Variant of {@link #testArea_rank_and_area_1()} with alternate source references to check the
|
367
|
* suppression of duplicates.
|
368
|
*
|
369
|
* This test relies on {@link #testArea_rank_and_area_1()}
|
370
|
* an makes assertions only on the alternative source references
|
371
|
* @throws JvmLimitsException
|
372
|
*/
|
373
|
@Test
|
374
|
@DataSets({
|
375
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
|
376
|
@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),
|
377
|
@DataSet(value="TransmissionEngineDistributionTest.xml"),
|
378
|
})
|
379
|
public void testArea_rank_and_area_3() throws JvmLimitsException {
|
380
|
|
381
|
Set<Distribution> distributions_LCA = new HashSet<Distribution>();
|
382
|
distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));
|
383
|
distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "3"));
|
384
|
|
385
|
addDistributions(
|
386
|
T_LAPSANA_COMMUNIS_ALPINA_UUID,
|
387
|
distributions_LCA
|
388
|
);
|
389
|
|
390
|
Set<Distribution> distributions_LC = new HashSet<>();
|
391
|
distributions_LC.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));
|
392
|
distributions_LC.add(newDistribution(book_b, yug_ko, PresenceAbsenceTerm.NATIVE(), "2"));
|
393
|
|
394
|
addDistributions(
|
395
|
T_LAPSANA_COMMUNIS_UUID,
|
396
|
distributions_LC
|
397
|
);
|
398
|
|
399
|
engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);
|
400
|
|
401
|
Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);
|
402
|
int computedDescriptionsCnt = 0;
|
403
|
for(TaxonDescription description : lapsana_communis.getDescriptions()) {
|
404
|
if(description.hasMarker(MarkerType.COMPUTED(), true)) {
|
405
|
computedDescriptionsCnt++;
|
406
|
assertEquals(2, description.getElements().size());
|
407
|
for(DescriptionElementBase distribution : description.getElements()) {
|
408
|
logger.debug(((Distribution)distribution).getArea() + " " + sourcesToString(distribution));
|
409
|
if(((Distribution)distribution).getArea().equals(yug_ko)){
|
410
|
assertEquals(2, distribution.getSources().size());
|
411
|
}
|
412
|
if(((Distribution)distribution).getArea().equals(yug)){
|
413
|
assertEquals(3, distribution.getSources().size());
|
414
|
}
|
415
|
}
|
416
|
}
|
417
|
}
|
418
|
assertEquals(1, computedDescriptionsCnt);
|
419
|
}
|
420
|
|
421
|
/**
|
422
|
* Variant of {@link #testArea_rank_and_area_1()} with alternate source references to
|
423
|
* check the handling of the case where the target taxon already has the distribution which is the
|
424
|
* result of the aggregation (see http://dev.e-taxonomy.eu/trac/ticket/4366#comment:12)
|
425
|
*
|
426
|
* This test relies on {@link #testArea_rank_and_area_1()}
|
427
|
* an makes assertions only on the alternative source references
|
428
|
* @throws JvmLimitsException
|
429
|
*/
|
430
|
@Test
|
431
|
@Ignore
|
432
|
@DataSets({
|
433
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="/eu/etaxonomy/cdm/database/ClearDB_with_Terms_DataSet.xml"),
|
434
|
@DataSet(value="/eu/etaxonomy/cdm/database/TermsDataSet-with_auditing_info.xml"),
|
435
|
@DataSet(value="TransmissionEngineDistributionTest.xml"),
|
436
|
})
|
437
|
public void testArea_rank_and_area_4() throws JvmLimitsException {
|
438
|
|
439
|
Set<Distribution> distributions_LCA = new HashSet<>();
|
440
|
distributions_LCA.add(newDistribution(book_a, yug_ko, PresenceAbsenceTerm.NATIVE(), "1"));
|
441
|
|
442
|
addDistributions(
|
443
|
T_LAPSANA_COMMUNIS_ALPINA_UUID,
|
444
|
distributions_LCA
|
445
|
);
|
446
|
|
447
|
Set<Distribution> distributions_LC = new HashSet<>();
|
448
|
distributions_LC.add(newDistribution(book_a, yug, PresenceAbsenceTerm.NATIVE(), "2")); // should succeed
|
449
|
|
450
|
addDistributions(
|
451
|
T_LAPSANA_COMMUNIS_UUID,
|
452
|
distributions_LC
|
453
|
);
|
454
|
|
455
|
engine.accumulate(AggregationMode.byAreasAndRanks, superAreas, lowerRank, upperRank, null, null);
|
456
|
|
457
|
Taxon lapsana_communis = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);
|
458
|
int computedDescriptionsCnt = 0;
|
459
|
for(TaxonDescription description : lapsana_communis.getDescriptions()) {
|
460
|
if(description.hasMarker(MarkerType.COMPUTED(), true)) {
|
461
|
computedDescriptionsCnt++;
|
462
|
assertEquals(2, description.getElements().size());
|
463
|
Distribution distribution = (Distribution)description.getElements().iterator().next();
|
464
|
if(distribution.getArea().equals(yug_ko)){
|
465
|
assertEquals(2, distribution.getSources().size());
|
466
|
DescriptionElementSource source = distribution.getSources().iterator().next();
|
467
|
assertEquals("2", source.getCitationMicroReference());
|
468
|
}
|
469
|
}
|
470
|
}
|
471
|
assertEquals(1, computedDescriptionsCnt);
|
472
|
}
|
473
|
|
474
|
/**
|
475
|
* @param referenceTitle
|
476
|
* @param area
|
477
|
* @param status
|
478
|
* @param microCitation
|
479
|
* @return
|
480
|
*/
|
481
|
private Distribution newDistribution(Reference reference, NamedArea area, PresenceAbsenceTerm status,
|
482
|
String microCitation) {
|
483
|
DescriptionElementSource source = DescriptionElementSource.NewPrimarySourceInstance(reference, microCitation);
|
484
|
Distribution distribution = Distribution.NewInstance(area, status);
|
485
|
distribution.getSources().add(source);
|
486
|
return distribution;
|
487
|
}
|
488
|
|
489
|
/**
|
490
|
* creates a new description for the taxon identified by the UUIDs
|
491
|
* @param taxonUuid
|
492
|
* @param distributions
|
493
|
*/
|
494
|
private void addDistributions(UUID taxonUuid, Collection<Distribution> distributions) {
|
495
|
Taxon taxon = (Taxon) taxonService.load(taxonUuid);
|
496
|
if(taxon == null) {
|
497
|
throw new NullPointerException("No taxon found for " + taxonUuid);
|
498
|
}
|
499
|
TaxonDescription description = TaxonDescription.NewInstance(taxon);
|
500
|
|
501
|
for (Distribution distribution : distributions) {
|
502
|
description.addElement(distribution);
|
503
|
}
|
504
|
taxonService.saveOrUpdate(taxon);
|
505
|
// need to write to database for transmission engine
|
506
|
commitAndStartNewTransaction(null);
|
507
|
}
|
508
|
|
509
|
private String sourcesToString(DescriptionElementBase deb) {
|
510
|
StringBuffer out = new StringBuffer();
|
511
|
for ( DescriptionElementSource source : deb.getSources()) {
|
512
|
out.append(source.getCitation().getTitle() + " : " + source.getCitationMicroReference() + ", ");
|
513
|
}
|
514
|
return out.toString();
|
515
|
}
|
516
|
|
517
|
|
518
|
//@Test // uncomment to create test data file//
|
519
|
@Override
|
520
|
public void createTestDataSet() throws FileNotFoundException {
|
521
|
|
522
|
// --- References --- //
|
523
|
Reference sec = ReferenceFactory.newDatabase();
|
524
|
sec.setTitleCache("Test", true);
|
525
|
Reference nomRef = ReferenceFactory.newBook();
|
526
|
sec.setTitleCache("Sp.Pl.", true);
|
527
|
|
528
|
referenceService.save(sec);
|
529
|
referenceService.save(nomRef);
|
530
|
|
531
|
|
532
|
// --- Taxa --- //
|
533
|
// Lapsana
|
534
|
// L. communis
|
535
|
// L. communis subsp. communis
|
536
|
// L. communis subsp. adenophora
|
537
|
// L. communis subsp. alpina
|
538
|
// Sonchella
|
539
|
// S. dentata
|
540
|
// S. stenoma
|
541
|
IBotanicalName n_lapsana = TaxonNameFactory.NewBotanicalInstance(Rank.GENUS());
|
542
|
n_lapsana.setTitleCache("Lapsana", true);
|
543
|
Taxon t_lapsana = Taxon.NewInstance(n_lapsana, sec);
|
544
|
t_lapsana.setUuid(T_LAPSANA_UUID);
|
545
|
taxonService.saveOrUpdate(t_lapsana);
|
546
|
|
547
|
IBotanicalName n_lapsana_communis = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
548
|
n_lapsana_communis.setTitleCache("L. communis", true);
|
549
|
Taxon t_lapsana_communis = Taxon.NewInstance(n_lapsana_communis, sec);
|
550
|
t_lapsana_communis.setUuid(T_LAPSANA_COMMUNIS_UUID);
|
551
|
taxonService.saveOrUpdate(t_lapsana_communis);
|
552
|
|
553
|
IBotanicalName n_lapsana_communis_communis = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES());
|
554
|
n_lapsana_communis_communis.setTitleCache("L. communis subsp. communis", true);
|
555
|
Taxon t_lapsana_communis_communis = Taxon.NewInstance(n_lapsana_communis_communis, sec);
|
556
|
t_lapsana_communis_communis.setUuid(T_LAPSANA_COMMUNIS_COMMUNIS_UUID);
|
557
|
taxonService.saveOrUpdate(t_lapsana_communis_communis);
|
558
|
|
559
|
IBotanicalName n_lapsana_communis_adenophora = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES());
|
560
|
n_lapsana_communis_adenophora.setTitleCache("L. communis subsp. adenophora", true);
|
561
|
Taxon t_lapsana_communis_adenophora = Taxon.NewInstance(n_lapsana_communis_adenophora, sec);
|
562
|
t_lapsana_communis_adenophora.setUuid(T_LAPSANA_COMMUNIS_ADENOPHORA_UUID);
|
563
|
taxonService.saveOrUpdate(t_lapsana_communis_adenophora);
|
564
|
|
565
|
IBotanicalName n_lapsana_communis_alpina = TaxonNameFactory.NewBotanicalInstance(Rank.SUBSPECIES());
|
566
|
n_lapsana_communis_alpina.setTitleCache("L. communis subsp. alpina", true);
|
567
|
Taxon t_lapsana_communis_alpina = Taxon.NewInstance(n_lapsana_communis_alpina, sec);
|
568
|
t_lapsana_communis_alpina.setUuid(T_LAPSANA_COMMUNIS_ALPINA_UUID);
|
569
|
taxonService.saveOrUpdate(t_lapsana_communis_alpina);
|
570
|
|
571
|
// --- Classification --- //
|
572
|
Classification classification = Classification.NewInstance("TestClassification");
|
573
|
classification.setUuid(CLASSIFICATION_UUID);
|
574
|
classificationService.save(classification);
|
575
|
TaxonNode node_lapsana = classification.addChildTaxon(t_lapsana, sec, null);
|
576
|
TaxonNode node_lapsana_communis = node_lapsana.addChildTaxon(t_lapsana_communis, sec, null);
|
577
|
node_lapsana_communis.addChildTaxon(t_lapsana_communis_communis, sec, null);
|
578
|
node_lapsana_communis.addChildTaxon(t_lapsana_communis_adenophora, sec, null);
|
579
|
node_lapsana_communis.addChildTaxon(t_lapsana_communis_alpina, sec, null);
|
580
|
classificationService.saveOrUpdate(classification);
|
581
|
|
582
|
// --- Distributions --- //
|
583
|
// tdwg3 level YUG : Yugoslavia
|
584
|
// contains tdwg4 level areas :
|
585
|
// YUG-BH Bosnia-Herzegovina
|
586
|
// YUG-CR Croatia
|
587
|
// YUG-KO Kosovo
|
588
|
// YUG-MA Macedonia
|
589
|
// YUG-MN Montenegro
|
590
|
|
591
|
// assigning distribution information to taxa
|
592
|
// expectations regarding the aggregation can be found in the comments below
|
593
|
// TaxonDescription d_lapsana_communis_communis = TaxonDescription.NewInstance(t_lapsana_communis_communis);
|
594
|
// d_lapsana_communis_communis.addElement(Distribution.NewInstance(
|
595
|
// TdwgArea.getAreaByTdwgAbbreviation("YUG-MN"),
|
596
|
// PresenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA() // should be ignored
|
597
|
// );
|
598
|
|
599
|
commitAndStartNewTransaction(null);
|
600
|
|
601
|
writeDbUnitDataSetFile(new String[] {
|
602
|
"TAXONBASE", "TAXONNAME",
|
603
|
"REFERENCE", "DESCRIPTIONELEMENTBASE", "DESCRIPTIONBASE",
|
604
|
"AGENTBASE", "CLASSIFICATION", "TAXONNODE",
|
605
|
"HOMOTYPICALGROUP", "LANGUAGESTRING",
|
606
|
"HIBERNATE_SEQUENCES"
|
607
|
});
|
608
|
|
609
|
}
|
610
|
|
611
|
}
|