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// $Id$
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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;
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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.util.Arrays;
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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.Test;
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import org.unitils.dbunit.annotation.DataSet;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution;
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import eu.etaxonomy.cdm.api.service.description.TransmissionEngineDistribution.AggregationMode;
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import eu.etaxonomy.cdm.model.common.Extension;
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import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
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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.BotanicalName;
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import eu.etaxonomy.cdm.model.name.Rank;
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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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* @date Feb 26, 2013
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*
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*/
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public class TransmissionEngineDistributionTest extends CdmTransactionalIntegrationTest {
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@SuppressWarnings("unused")
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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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@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.SPECIES();
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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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engine.updatePriorities();
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}
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@Test
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@DataSet
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public void testPriorities() throws FileNotFoundException {
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Set extensions = termService.load(PresenceAbsenceTerm.CULTIVATED().getUuid()).getExtensions();
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assertEquals(TransmissionEngineDistribution.EXTENSION_VALUE_PREFIX + "45", ((Extension)extensions.iterator().next()).getValue());
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void test_ignore() throws FileNotFoundException {
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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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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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testArea_area() {
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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new Distribution[] {
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Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.CULTIVATED()),
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Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.NATIVE()), // should succeed
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Distribution.NewInstance(yug_bh, PresenceAbsenceTerm.INTRODUCED())
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}
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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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boolean expectedAreaFound = false;
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for (TaxonDescription description : lapsana_communis_alpina.getDescriptions()) {
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Distribution distribution = (Distribution) description.getElements().iterator().next(); // only one aggregated area expected
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if(distribution.getArea().equals(yug)) {
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expectedAreaFound = true;
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assertEquals("aggregated status of area YUG is wrong", PresenceAbsenceTerm.NATIVE().getLabel(), distribution.getStatus().getLabel());
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}
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}
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assertTrue("The areae YUG should have been found", expectedAreaFound);
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}
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@Test
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@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class)
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public void testArea_rank_and_area() {
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addDistributions(
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T_LAPSANA_COMMUNIS_ALPINA_UUID,
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new Distribution[] {
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Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.CULTIVATED()),
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Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.NATIVE()), // should succeed
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}
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);
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addDistributions(
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T_LAPSANA_COMMUNIS_UUID,
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new Distribution[] {
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Distribution.NewInstance(yug_mn, PresenceAbsenceTerm.INTRODUCED_UNCERTAIN_DEGREE_OF_NATURALISATION()),
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Distribution.NewInstance(yug_ko, PresenceAbsenceTerm.CULTIVATED()),
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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 = (Taxon) taxonService.load(T_LAPSANA_COMMUNIS_UUID);
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assertEquals(2, lapsana_communis.getDescriptions().size());
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Taxon lapsana = (Taxon) taxonService.load(T_LAPSANA_UUID);
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assertEquals(1, lapsana.getDescriptions().size());
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TaxonDescription description = lapsana.getDescriptions().iterator().next();
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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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}
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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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}
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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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}
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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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* creates a new description for the taxon identified by the UUIDs
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* @param taxonUuid
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* @param distributions
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*/
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private void addDistributions(UUID taxonUuid, Distribution[] distributions) {
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Taxon taxon = (Taxon) taxonService.load(taxonUuid);
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if(taxon == null) {
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throw new NullPointerException("No taxon found for " + taxonUuid);
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}
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TaxonDescription description = TaxonDescription.NewInstance(taxon);
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for (Distribution distribution : distributions) {
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description.addElement(distribution);
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}
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taxonService.saveOrUpdate(taxon);
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// need to write to database for transmission engine
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commitAndStartNewTransaction(null);
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}
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// @Test // uncomment to create test data file//
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@Override
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public void createTestDataSet() throws FileNotFoundException {
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// --- References --- //
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Reference sec = ReferenceFactory.newDatabase();
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sec.setTitleCache("Test", true);
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Reference nomRef = ReferenceFactory.newBook();
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sec.setTitleCache("Sp.Pl.", true);
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referenceService.save(sec);
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referenceService.save(nomRef);
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// --- Taxa --- //
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// Lapsana
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// L. communis
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// L. communis subsp. communis
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// L. communis subsp. adenophora
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// L. communis subsp. alpina
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// Sonchella
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// S. dentata
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// S. stenoma
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BotanicalName n_lapsana = BotanicalName.NewInstance(Rank.GENUS());
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n_lapsana.setTitleCache("Lapsana", true);
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Taxon t_lapsana = Taxon.NewInstance(n_lapsana, sec);
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t_lapsana.setUuid(T_LAPSANA_UUID);
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taxonService.saveOrUpdate(t_lapsana);
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BotanicalName n_lapsana_communis = BotanicalName.NewInstance(Rank.SPECIES());
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n_lapsana_communis.setTitleCache("L. communis", true);
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Taxon t_lapsana_communis = Taxon.NewInstance(n_lapsana_communis, sec);
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t_lapsana_communis.setUuid(T_LAPSANA_COMMUNIS_UUID);
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taxonService.saveOrUpdate(t_lapsana_communis);
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BotanicalName n_lapsana_communis_communis = BotanicalName.NewInstance(Rank.SUBSPECIES());
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n_lapsana_communis_communis.setTitleCache("L. communis subsp. communis", true);
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Taxon t_lapsana_communis_communis = Taxon.NewInstance(n_lapsana_communis_communis, sec);
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t_lapsana_communis_communis.setUuid(T_LAPSANA_COMMUNIS_COMMUNIS_UUID);
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taxonService.saveOrUpdate(t_lapsana_communis_communis);
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BotanicalName n_lapsana_communis_adenophora = BotanicalName.NewInstance(Rank.SUBSPECIES());
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n_lapsana_communis_adenophora.setTitleCache("L. communis subsp. adenophora", true);
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Taxon t_lapsana_communis_adenophora = Taxon.NewInstance(n_lapsana_communis_adenophora, sec);
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t_lapsana_communis_adenophora.setUuid(T_LAPSANA_COMMUNIS_ADENOPHORA_UUID);
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taxonService.saveOrUpdate(t_lapsana_communis_adenophora);
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BotanicalName n_lapsana_communis_alpina = BotanicalName.NewInstance(Rank.SUBSPECIES());
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n_lapsana_communis_alpina.setTitleCache("L. communis subsp. alpina", true);
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Taxon t_lapsana_communis_alpina = Taxon.NewInstance(n_lapsana_communis_alpina, sec);
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t_lapsana_communis_alpina.setUuid(T_LAPSANA_COMMUNIS_ALPINA_UUID);
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taxonService.saveOrUpdate(t_lapsana_communis_alpina);
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// --- Classification --- //
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Classification classification = Classification.NewInstance("TestClassification");
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classification.setUuid(CLASSIFICATION_UUID);
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classificationService.save(classification);
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TaxonNode node_lapsana = classification.addChildTaxon(t_lapsana, sec, null);
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TaxonNode node_lapsana_communis = node_lapsana.addChildTaxon(t_lapsana_communis, sec, null);
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node_lapsana_communis.addChildTaxon(t_lapsana_communis_communis, sec, null);
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node_lapsana_communis.addChildTaxon(t_lapsana_communis_adenophora, sec, null);
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node_lapsana_communis.addChildTaxon(t_lapsana_communis_alpina, sec, null);
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classificationService.saveOrUpdate(classification);
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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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// assigning distribution information to taxa
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// expectations regarding the aggregation can be found in the comments below
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// TaxonDescription d_lapsana_communis_communis = TaxonDescription.NewInstance(t_lapsana_communis_communis);
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// d_lapsana_communis_communis.addElement(Distribution.NewInstance(
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// TdwgArea.getAreaByTdwgAbbreviation("YUG-MN"),
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// PresenceTerm.ENDEMIC_FOR_THE_RELEVANT_AREA() // should be ignored
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// );
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commitAndStartNewTransaction(null);
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writeDbUnitDataSetFile(new String[] {
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"TAXONBASE", "TAXONNAMEBASE",
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"REFERENCE", "DESCRIPTIONELEMENTBASE", "DESCRIPTIONBASE",
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"AGENTBASE", "CLASSIFICATION", "TAXONNODE",
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"HOMOTYPICALGROUP", "LANGUAGESTRING",
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});
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}
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}
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