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/**
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* Copyright (C) 2009 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.persistence.dao.hibernate.taxon;
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import static org.junit.Assert.assertEquals;
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import static org.junit.Assert.assertFalse;
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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 static org.junit.Assert.fail;
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import java.io.FileNotFoundException;
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import java.util.ArrayList;
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import java.util.HashSet;
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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.hibernate.Hibernate;
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import org.hibernate.envers.query.AuditEntity;
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import org.hibernate.envers.query.criteria.AuditCriterion;
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import org.hibernate.proxy.HibernateProxy;
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import org.junit.After;
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import org.junit.Assert;
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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.dbunit.annotation.ExpectedDataSet;
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import org.unitils.spring.annotation.SpringBeanByType;
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import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
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import eu.etaxonomy.cdm.model.common.Marker;
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import eu.etaxonomy.cdm.model.common.MarkerType;
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import eu.etaxonomy.cdm.model.location.NamedArea;
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import eu.etaxonomy.cdm.model.name.TaxonName;
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import eu.etaxonomy.cdm.model.reference.Reference;
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import eu.etaxonomy.cdm.model.taxon.Classification;
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import eu.etaxonomy.cdm.model.taxon.Synonym;
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import eu.etaxonomy.cdm.model.taxon.SynonymType;
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import eu.etaxonomy.cdm.model.taxon.Taxon;
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import eu.etaxonomy.cdm.model.taxon.TaxonBase;
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import eu.etaxonomy.cdm.model.taxon.TaxonNode;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationship;
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import eu.etaxonomy.cdm.model.taxon.TaxonRelationshipType;
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import eu.etaxonomy.cdm.model.view.AuditEvent;
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import eu.etaxonomy.cdm.model.view.AuditEventRecord;
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import eu.etaxonomy.cdm.model.view.context.AuditEventContextHolder;
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import eu.etaxonomy.cdm.persistence.dao.common.AuditEventSort;
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import eu.etaxonomy.cdm.persistence.dao.common.IDefinedTermDao;
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import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
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import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
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import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
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import eu.etaxonomy.cdm.persistence.query.GroupByCount;
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import eu.etaxonomy.cdm.persistence.query.GroupByDate;
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import eu.etaxonomy.cdm.persistence.query.Grouping;
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import eu.etaxonomy.cdm.persistence.query.MatchMode;
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import eu.etaxonomy.cdm.persistence.query.NativeSqlOrderHint;
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import eu.etaxonomy.cdm.persistence.query.OrderHint;
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import eu.etaxonomy.cdm.persistence.query.OrderHint.SortOrder;
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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.mueller
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* @author ben.clark
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*/
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public class TaxonDaoHibernateImplTest extends CdmTransactionalIntegrationTest {
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@SpringBeanByType
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private ITaxonDao taxonDao;
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@SpringBeanByType
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private ITaxonNodeDao taxonNodeDao;
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@SpringBeanByType
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private IClassificationDao classificationDao;
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@SpringBeanByType
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private IReferenceDao referenceDao;
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@SpringBeanByType
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private IDefinedTermDao definedTermDao;
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private UUID uuid = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
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private UUID sphingidae = UUID.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9");
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private UUID acherontia = UUID.fromString("c5cc8674-4242-49a4-aada-72d63194f5fa");
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private UUID rethera = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
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private UUID retheraSecCdmtest = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
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private UUID atroposAgassiz = UUID.fromString("d75b2e3d-7394-4ada-b6a5-93175b8751c1"); // a Synonym
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private UUID atroposOken = UUID.fromString("6bfedf25-6dbc-4d5c-9d56-84f9052f3b2a"); // a Synonym
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private UUID atroposLeach = UUID.fromString("3da4ab34-6c50-4586-801e-732615899b07"); // a Synonym
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private UUID acherontiaLachesis = UUID.fromString("b04cc9cb-2b4a-4cc4-a94a-3c93a2158b06");
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private UUID aus = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
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private UUID UUID_ACHERONTIA_NODE = UUID.fromString("56b10cf0-9522-407e-9f90-0c2dba263c94");
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private UUID UUID_CLASSIFICATION2 = UUID.fromString("a71467a6-74dc-4148-9530-484628a5ab0e");
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private AuditEvent previousAuditEvent;
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private AuditEvent mostRecentAuditEvent;
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private UUID northernAmericaUuid;
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private UUID southernAmericaUuid;
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private UUID classificationUuid;
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private boolean includeUnpublished = true;
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private boolean NO_UNPUBLISHED = false;
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private static final boolean doTaxa = true;
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private static final boolean noTaxa = false;
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private static final boolean doSynonyms = true;
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private static final boolean noSynonyms = false;
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private static final boolean doMisapplied = true;
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private static final boolean noMisapplied = false;
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private static final boolean doCommonNames = true;
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private static final boolean noCommonNames = false;
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@SuppressWarnings("unused")
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private static final String[] TABLE_NAMES = new String[] {
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"HOMOTYPICALGROUP", "HOMOTYPICALGROUP_AUD", "REFERENCE", "REFERENCE_AUD", "TAXONBASE", "TAXONBASE_AUD"
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, "TAXONNAME", "TAXONNAME_AUD", "TAXONRELATIONSHIP", "TAXONRELATIONSHIP_AUD" };
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@Before
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public void setUp() {
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previousAuditEvent = new AuditEvent();
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previousAuditEvent.setRevisionNumber(1025);
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previousAuditEvent.setUuid(UUID.fromString("a680fab4-365e-4765-b49e-768f2ee30cda"));
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mostRecentAuditEvent = new AuditEvent();
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mostRecentAuditEvent.setRevisionNumber(1026);
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mostRecentAuditEvent.setUuid(UUID.fromString("afe8e761-8545-497b-9134-6a6791fc0b0d"));
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AuditEventContextHolder.clearContext(); // By default we're in the current view (i.e. view == null)
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northernAmericaUuid = UUID.fromString("2757e726-d897-4546-93bd-7951d203bf6f");
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southernAmericaUuid = UUID.fromString("6310b3ba-96f4-4855-bb5b-326e7af188ea");
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classificationUuid = UUID.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9");
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includeUnpublished = true;
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}
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@After
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public void tearDown() {
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AuditEventContextHolder.clearContext();
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}
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/**
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* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#TaxonDaoHibernateImpl()}.
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*/
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@Test
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@DataSet
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public void testInit() {
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logger.warn("testInit()");
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assertNotNull("Instance of ITaxonDao expected",taxonDao);
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assertNotNull("Instance of IReferenceDao expected",referenceDao);
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}
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@Test
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@DataSet
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public void testGetTaxaByName() {
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includeUnpublished= true;
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boolean accepted = true;
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Reference sec = referenceDao.findById(1);
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assert sec != null : "sec must exist";
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@SuppressWarnings("rawtypes")
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List<TaxonBase> results = taxonDao.getTaxaByName("Aus", includeUnpublished, sec);
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assertNotNull("getTaxaByName should return a List", results);
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//assertFalse("The list should not be empty", results.isEmpty());
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assertEquals(1, results.size());
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results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, accepted, includeUnpublished, null, null);
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assertNotNull("getTaxaByName should return a List", results);
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int numberOfTaxaByName_A = 5;
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//logger.setLevel(Level.DEBUG); //FIXME #######################
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if (logger.isDebugEnabled()) {
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for (int i = 0; i < results.size(); i++) {
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String nameCache = "";
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TaxonName taxonName= results.get(i).getName();
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nameCache = taxonName.getNameCache();
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logger.debug(results.get(i).getClass() + "(" + i +")" +
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": Name Cache = " + nameCache + ", Title Cache = " + results.get(i).getTitleCache());
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}
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}
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assertEquals(numberOfTaxaByName_A, results.size());
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includeUnpublished = false;
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results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, accepted, includeUnpublished, null, null);
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assertEquals(numberOfTaxaByName_A, results.size()); // no unpublished yet
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//System.err.println("Species group: " + Rank.SPECIESGROUP().getId() + "Species: " + Rank.SPECIES().getId() + "Section Botany: "+ Rank.SECTION_BOTANY());
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// assertEquals(results.get(0).getTitleCache(), "Abies sec. ???");
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// assertEquals(results.get(1).getTitleCache(), "Abies Mill.");
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// assertEquals(results.get(2).getTitleCache(), "Abies mill. sec. ???");
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// assertEquals(results.get(3).getTitleCache(), "Abies alba sec. ???");
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// assertEquals(results.get(4).getTitleCache(), "Abies alba Michx. sec. ???");
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// assertEquals(results.get(5).getTitleCache(), "Abies alba Mill. sec. ???");
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includeUnpublished = true;
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results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, accepted, includeUnpublished, null, null);
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assertNotNull("getTaxaByName should return a List", results);
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assertEquals(numberOfTaxaByName_A, results.size());
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results = taxonDao.getTaxaByName("Aus", MatchMode.EXACT, accepted, includeUnpublished, null, null);
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assertNotNull("getTaxaByName should return a List", results);
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assertEquals("Results list should contain one entity",1,results.size());
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}
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@Test
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@DataSet (loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
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public void testGetTaxaByNameWithMisappliedNames(){
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Classification classification = classificationDao.load(classificationUuid);
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TaxonNode subtree = null;
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/* NOTE:
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* The testdata contains 3 misapplied names (1. nameCache = Aus, 2. nameCache = Rethera, 3. nameCache = Daphnis),
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* two contained in the classification used in this test,
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* the other one is not contained in any classification. This later case is the more general situation.
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* Misapplied names should be found regardless of whether they are contained in a classification or not.
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*/
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//two accepted taxa starting with R in classification "TestBaum"
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@SuppressWarnings("rawtypes")
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List<TaxonBase> results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "R*", classification, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 2 Taxa", 2, results.size());
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//three taxa, 2 accepted and 1 misapplied name starting with R
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results = taxonDao.getTaxaByName(doTaxa, noSynonyms, doMisapplied, noCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 3 Taxa", 3, results.size());
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//one synonym has no accepted taxon
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results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "A*", null, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 11 Taxa",11, results.size());
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//two accepted taxa in classification and 1 misapplied name with accepted name in classification
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results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", classification, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 3 Taxa", 3, results.size());
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//same with unpublished
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includeUnpublished = false;
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results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", classification, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 3 Taxa", 3, results.size());
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includeUnpublished = true;
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//same as above because all taxa, synonyms and misapplied names starting with R are in the classification
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results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 3 Taxa", 3, results.size());
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//find misapplied names with accepted taxon in the classification, the accepted taxa of two misapplied names are in the classification
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results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "*", classification, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 2 Taxa", 2, results.size());
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//find misapplied names beginning with R
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results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 1 Taxa", 1, results.size());
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//find all three misapplied names
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results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "*", null, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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Assert.assertEquals("There should be 3 Taxa", 3, results.size());
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}
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/**
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* Test for all not covered possibilities of searches
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*/
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@Test
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@DataSet (loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
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public void testGetTaxaByNameVariants(){
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TaxonNode subtree = null;
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@SuppressWarnings("rawtypes")
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List<TaxonBase> results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
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null, includeUnpublished, null, null, null, null);
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300
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Assert.assertEquals("There should be 2 Taxa",2, results.size());
|
|
301
|
|
|
302
|
results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, doCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
|
|
303
|
null, includeUnpublished, null, null, null, null);
|
|
304
|
Assert.assertEquals("There should be 1 Taxa", 1, results.size());
|
|
305
|
|
|
306
|
results = taxonDao.getTaxaByName(noTaxa, doSynonyms, doMisapplied, doCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
|
|
307
|
null, includeUnpublished, null, null, null, null);
|
|
308
|
Assert.assertEquals("There should be 1 Taxa", 1, results.size());
|
|
309
|
|
|
310
|
results = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
|
|
311
|
null, includeUnpublished, null, null, null, null);
|
|
312
|
Assert.assertEquals("There should be 2 Taxa", 2, results.size());
|
|
313
|
|
|
314
|
results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
|
|
315
|
null, includeUnpublished, null, null, null, null);
|
|
316
|
Assert.assertEquals("There should be 2 Taxa", 2, results.size());
|
|
317
|
|
|
318
|
Classification classification = classificationDao.load(classificationUuid);
|
|
319
|
results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", classification, subtree, MatchMode.BEGINNING,
|
|
320
|
null, includeUnpublished, null, null, null, null);
|
|
321
|
Assert.assertEquals("There should be 1 Taxa", 1, results.size());
|
|
322
|
|
|
323
|
Set<NamedArea> namedAreas = new HashSet<>();
|
|
324
|
namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
|
|
325
|
results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
|
|
326
|
namedAreas, includeUnpublished, null, null, null, null);
|
|
327
|
Assert.assertEquals("There should be 1 Taxa", 1, results.size());
|
|
328
|
}
|
|
329
|
|
|
330
|
/**
|
|
331
|
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
|
|
332
|
*/
|
|
333
|
@Test
|
|
334
|
@DataSet
|
|
335
|
public void testGetTaxaByNameForEditor() {
|
|
336
|
TaxonNode subtree = null;
|
|
337
|
Reference sec = referenceDao.findById(1);
|
|
338
|
assert sec != null : "sec must exist";
|
|
339
|
|
|
340
|
@SuppressWarnings("rawtypes")
|
|
341
|
List<UuidAndTitleCache<? extends IdentifiableEntity>> results = taxonDao.getTaxaByNameForEditor(
|
|
342
|
doTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "Acher", null, subtree, MatchMode.BEGINNING, null, null);
|
|
343
|
assertNotNull("getTaxaByName should return a List", results);
|
|
344
|
assertFalse("The list should not be empty", results.isEmpty());
|
|
345
|
assertEquals(4, results.size());
|
|
346
|
|
|
347
|
|
|
348
|
results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,includeUnpublished, "A",null, subtree, MatchMode.BEGINNING, null, null);
|
|
349
|
assertNotNull("getTaxaByName should return a List", results);
|
|
350
|
assertEquals(7, results.size());
|
|
351
|
|
|
352
|
|
|
353
|
results = taxonDao.getTaxaByNameForEditor(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
|
|
354
|
assertNotNull("getTaxaByName should return a List", results);
|
|
355
|
assertEquals(5, results.size());
|
|
356
|
assertEquals(results.get(0).getType(), Taxon.class);
|
|
357
|
|
|
358
|
results = taxonDao.getTaxaByNameForEditor(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
|
|
359
|
assertNotNull("getTaxaByName should return a List", results);
|
|
360
|
assertEquals(2, results.size());
|
|
361
|
assertEquals(results.get(0).getType(), Synonym.class);
|
|
362
|
|
|
363
|
results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,includeUnpublished, "Aus", null, subtree, MatchMode.EXACT, null, null);
|
|
364
|
assertNotNull("getTaxaByName should return a List", results);
|
|
365
|
assertEquals("Results list should contain one entity",1,results.size());
|
|
366
|
|
|
367
|
results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
|
|
368
|
assertNotNull("getTaxaByName should return a List", results);
|
|
369
|
assertEquals("Results list should contain one entity", 8, results.size());
|
|
370
|
|
|
371
|
//TODO: test the search for misapplied names
|
|
372
|
|
|
373
|
}
|
|
374
|
|
|
375
|
|
|
376
|
/**
|
|
377
|
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}
|
|
378
|
* restricting the search by a set of Areas.
|
|
379
|
*/
|
|
380
|
@Test
|
|
381
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
|
|
382
|
public void testGetTaxaByNameAndArea() {
|
|
383
|
TaxonNode subtree = null;
|
|
384
|
Set<NamedArea> namedAreas = new HashSet<>();
|
|
385
|
namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
|
|
386
|
//namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
|
|
387
|
//namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
|
|
388
|
|
|
389
|
Classification classification = classificationDao.findByUuid(classificationUuid);
|
|
390
|
|
|
391
|
// prepare some synonym relation ships for some tests
|
|
392
|
Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
|
|
393
|
Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
|
|
394
|
taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
|
|
395
|
// logger.warn("addSynonym(..)");
|
|
396
|
|
|
397
|
Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
|
|
398
|
Taxon taxonRetheraSecCdmTest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
|
|
399
|
taxonRetheraSecCdmTest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
|
|
400
|
this.taxonDao.save(taxonRetheraSecCdmTest);
|
|
401
|
|
|
402
|
Taxon test = (Taxon)this.taxonDao.findByUuid(retheraSecCdmtest);
|
|
403
|
// Set<Synonym> synonyms3 = test.getSynonyms();
|
|
404
|
// 1. searching for a taxon (Rethera)
|
|
405
|
//long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
|
|
406
|
|
|
407
|
@SuppressWarnings("rawtypes")
|
|
408
|
List<TaxonBase> results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", null, subtree, MatchMode.BEGINNING, namedAreas,
|
|
409
|
includeUnpublished, null, null, null, null);
|
|
410
|
assertNotNull("getTaxaByName should return a List", results);
|
|
411
|
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
|
|
412
|
|
|
413
|
results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "com*", null, subtree, MatchMode.BEGINNING, namedAreas,
|
|
414
|
includeUnpublished, null, null, null, null);
|
|
415
|
assertNotNull("getTaxaByName should return a List", results);
|
|
416
|
assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
|
|
417
|
|
|
418
|
// 2. searching for a taxon (Rethera) contained in a specific classification
|
|
419
|
results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", classification, subtree, MatchMode.BEGINNING, namedAreas,
|
|
420
|
includeUnpublished, null, null, null, null);
|
|
421
|
assertNotNull("getTaxaByName should return a List", results);
|
|
422
|
assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
|
|
423
|
|
|
424
|
|
|
425
|
// 3. searching for Synonyms
|
|
426
|
results = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Atropo", null, subtree, MatchMode.ANYWHERE, null,
|
|
427
|
includeUnpublished, null, null, null, null);
|
|
428
|
assertNotNull("getTaxaByName should return a List", results);
|
|
429
|
/*System.err.println(results.get(0).getTitleCache() + " - " +results.get(1).getTitleCache() + " - " +results.get(2).getTitleCache() );
|
|
430
|
|
|
431
|
|
|
432
|
System.err.println(((Synonym)results.get(0)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(1)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(2)).getAcceptedTaxa().contains(taxonRethera)+ " - " );
|
|
433
|
*/
|
|
434
|
assertTrue("expected to find three taxa but found "+results.size(), results.size() == 3);
|
|
435
|
|
|
436
|
// 4. searching for Synonyms
|
|
437
|
results = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false,"Atropo", null, subtree, MatchMode.BEGINNING, null,
|
|
438
|
includeUnpublished, null, null, null, null);
|
|
439
|
assertNotNull("getTaxaByName should return a List", results);
|
|
440
|
assertTrue("expected to find three taxa but found "+results.size(), results.size() == 3);
|
|
441
|
|
|
442
|
|
|
443
|
// 5. searching for a Synonyms and Taxa
|
|
444
|
results = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"A", null, subtree, MatchMode.BEGINNING, namedAreas,
|
|
445
|
includeUnpublished, null, null, null, null);
|
|
446
|
//only five taxa have a distribution
|
|
447
|
assertNotNull("getTaxaByName should return a List", results);
|
|
448
|
assertTrue("expected to find 8 taxa but found "+results.size(), results.size() == 8);
|
|
449
|
}
|
|
450
|
|
|
451
|
|
|
452
|
/**
|
|
453
|
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#findByNameTitleCache(Class<? extends TaxonBase>clazz, String queryString, Classification classification, TaxonNode subtree, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths)}
|
|
454
|
* restricting the search by a set of Areas.
|
|
455
|
*/
|
|
456
|
@Test
|
|
457
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
|
|
458
|
public void testFindByNameTitleCache() {
|
|
459
|
TaxonNode subtree = null;
|
|
460
|
|
|
461
|
Set<NamedArea> namedAreas = new HashSet<>();
|
|
462
|
namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
|
|
463
|
//namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
|
|
464
|
//namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
|
|
465
|
|
|
466
|
Classification classification = classificationDao.findByUuid(classificationUuid);
|
|
467
|
|
|
468
|
// prepare some synonym relation ships for some tests
|
|
469
|
Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
|
|
470
|
Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
|
|
471
|
taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
|
|
472
|
//logger.warn("addSynonym(..)");
|
|
473
|
this.taxonDao.clear();
|
|
474
|
Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
|
|
475
|
Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
|
|
476
|
taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
|
|
477
|
this.taxonDao.clear();
|
|
478
|
|
|
479
|
// 1. searching for a taxon (Rethera)
|
|
480
|
//long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
|
|
481
|
|
|
482
|
@SuppressWarnings("rawtypes")
|
|
483
|
List<TaxonBase> results = taxonDao.findByNameTitleCache(doTaxa, noSynonyms, includeUnpublished, "Rethera Rothschild & Jordan, 1903", null, subtree, MatchMode.EXACT, namedAreas,
|
|
484
|
null, null, null, null);
|
|
485
|
assertNotNull("getTaxaByName should return a List", results);
|
|
486
|
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
|
|
487
|
|
|
488
|
// 2. searching for a taxon (Rethera) contained in a specific classification
|
|
489
|
results = taxonDao.findByNameTitleCache(doTaxa, noSynonyms, includeUnpublished, "Rethera Rothschild & Jordan, 1903", classification, subtree, MatchMode.EXACT, namedAreas,
|
|
490
|
null, null, null, null);
|
|
491
|
assertNotNull("getTaxaByName should return a List", results);
|
|
492
|
assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
|
|
493
|
|
|
494
|
// 3. searching for Synonyms
|
|
495
|
results = taxonDao.findByNameTitleCache(noTaxa, doSynonyms, includeUnpublished, "*Atropo", null, subtree, MatchMode.ANYWHERE, null,
|
|
496
|
null, null, null, null);
|
|
497
|
assertNotNull("getTaxaByName should return a List", results);
|
|
498
|
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
|
|
499
|
|
|
500
|
// 4. searching for Synonyms
|
|
501
|
results = taxonDao.findByNameTitleCache(noTaxa, doSynonyms, includeUnpublished, "Atropo", null, subtree, MatchMode.BEGINNING, null,
|
|
502
|
null, null, null, null);
|
|
503
|
assertNotNull("getTaxaByName should return a List", results);
|
|
504
|
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
|
|
505
|
|
|
506
|
// 5. searching for a Synonyms and Taxa
|
|
507
|
// attache a synonym first
|
|
508
|
Synonym syn = (Synonym)taxonDao.findByUuid(this.atroposLeach);
|
|
509
|
Taxon tax = (Taxon) taxonDao.findByUuid(rethera);
|
|
510
|
tax.addSynonym(syn, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
511
|
|
|
512
|
taxonDao.save(tax);
|
|
513
|
results = taxonDao.findByNameTitleCache(doTaxa, doSynonyms, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, namedAreas,
|
|
514
|
null, null, null, null);
|
|
515
|
assertNotNull("getTaxaByName should return a List", results);
|
|
516
|
assertTrue("expected to find 8 taxa but found "+results.size(), results.size() == 8);
|
|
517
|
}
|
|
518
|
|
|
519
|
@Test
|
|
520
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
|
|
521
|
public void testTaxonNameInTwoClassifications(){
|
|
522
|
TaxonNode subtree = null;
|
|
523
|
List<String> propertyPaths = new ArrayList<>();
|
|
524
|
propertyPaths.add("taxonNodes");
|
|
525
|
@SuppressWarnings("rawtypes")
|
|
526
|
List<TaxonBase> taxa = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"P", null, subtree, MatchMode.BEGINNING,
|
|
527
|
null, includeUnpublished, null, null, null, null);
|
|
528
|
Taxon taxon = (Taxon)taxa.get(0);
|
|
529
|
Set<TaxonNode> nodes = taxon.getTaxonNodes();
|
|
530
|
assertTrue(nodes.size() == 1);
|
|
531
|
//assertNotNull(taxa);
|
|
532
|
//assertTrue(taxa.size() > 0);
|
|
533
|
}
|
|
534
|
|
|
535
|
@Test
|
|
536
|
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
|
|
537
|
public void testGetTaxaByNameProParteSynonym(){
|
|
538
|
TaxonNode subtree = null;
|
|
539
|
@SuppressWarnings("rawtypes")
|
|
540
|
List<TaxonBase> taxa = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", null,subtree,
|
|
541
|
MatchMode.BEGINNING, null, includeUnpublished, null, null, null, null);
|
|
542
|
Assert.assertEquals("2 synonyms and 1 pro parte synonym should be returned.", 3, taxa.size());
|
|
543
|
assertTrue("Pro parte should exist", existsInCollection(taxa, acherontiaLachesis));
|
|
544
|
assertTrue("Normal synonym should exist", existsInCollection(taxa, atroposAgassiz));
|
|
545
|
assertTrue("2. normal synonym should exist", existsInCollection(taxa, atroposOken));
|
|
546
|
//TODO shouldn't we also find orphaned synonyms (without accepted taxon) like Atropos Leach?
|
|
547
|
|
|
548
|
taxa = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", null,subtree,
|
|
549
|
MatchMode.BEGINNING, null, NO_UNPUBLISHED, null, null, null, null);
|
|
550
|
Assert.assertEquals("2 synonyms and no pro parte synonym should be returned.", 2, taxa.size());
|
|
551
|
assertTrue("Normal synonym should exist", existsInCollection(taxa, atroposAgassiz));
|
|
552
|
assertTrue("2. normal synonym should exist", existsInCollection(taxa, atroposOken));
|
|
553
|
|
|
554
|
taxa = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "A", null,subtree,
|
|
555
|
MatchMode.BEGINNING, null, includeUnpublished, null, null, null, null);
|
|
556
|
Assert.assertEquals("1 misapplied name, no pro parte synonym should be returned.", 1, taxa.size());
|
|
557
|
assertTrue("Pro parte should exist", existsInCollection(taxa, aus));
|
|
558
|
|
|
559
|
}
|
|
560
|
|
|
561
|
@Test
|
|
562
|
@DataSet
|
|
563
|
public void testFindByUuid() {
|
|
564
|
Taxon taxon = (Taxon)taxonDao.findByUuid(uuid);
|
|
565
|
assertNotNull("findByUuid should return a taxon", taxon);
|
|
566
|
assertFalse("findByUuid should not return a taxon with it's name initialized",Hibernate.isInitialized(taxon.getName()));
|
|
567
|
}
|
|
568
|
|
|
569
|
@Test
|
|
570
|
@DataSet
|
|
571
|
public void testLoad() {
|
|
572
|
List<String> propertyPaths = new ArrayList<>();
|
|
573
|
propertyPaths.add("name");
|
|
574
|
propertyPaths.add("sec");
|
|
575
|
Taxon taxon = (Taxon)taxonDao.load(uuid, propertyPaths);
|
|
576
|
assertNotNull("findByUuid should return a taxon",taxon);
|
|
577
|
assertTrue("load should return a taxon with it's name initialized, given that the property was specified in the method",Hibernate.isInitialized(taxon.getName()));
|
|
578
|
assertTrue("load should return a taxon with it's secundum reference initialized, given that the property was specified in the method",Hibernate.isInitialized(taxon.getSec()));
|
|
579
|
}
|
|
580
|
|
|
581
|
@Test
|
|
582
|
@DataSet
|
|
583
|
public void testCountTaxonRelationshipsByTaxon() {
|
|
584
|
Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
|
|
585
|
assert taxon != null : "taxon must exist";
|
|
586
|
|
|
587
|
long numberOfRelatedTaxa = taxonDao.countTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
588
|
includeUnpublished, TaxonRelationship.Direction.relatedTo);
|
|
589
|
assertEquals("countTaxonRelationships should return 8", 8, numberOfRelatedTaxa);
|
|
590
|
}
|
|
591
|
|
|
592
|
@Test
|
|
593
|
@DataSet
|
|
594
|
public void testCountTaxaByName() {
|
|
595
|
TaxonNode subtree = null;
|
|
596
|
Classification classification= null;
|
|
597
|
long numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames,false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
598
|
assertEquals(5, numberOfTaxa);
|
|
599
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "S", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
600
|
assertEquals("Sphingidae, Smerinthus, Smerinthus kindermannii and Sphingonaepiopsis expected", 4, numberOfTaxa);
|
|
601
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Smerinthus kindermannii", classification, subtree, MatchMode.EXACT, null, includeUnpublished);
|
|
602
|
assertEquals(1, numberOfTaxa);
|
|
603
|
numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
604
|
assertEquals(2, numberOfTaxa);
|
|
605
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
606
|
assertEquals(7, numberOfTaxa);
|
|
607
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Aasfwerfwf fffe", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
608
|
assertEquals(0, numberOfTaxa);
|
|
609
|
|
|
610
|
subtree = taxonNodeDao.findByUuid(UUID_ACHERONTIA_NODE);
|
|
611
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
612
|
assertEquals("Acherontia and 2 A. species expected", 3, numberOfTaxa);
|
|
613
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "S", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
614
|
assertEquals("", 0, numberOfTaxa);
|
|
615
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Smerinthus kindermannii", classification, subtree, MatchMode.EXACT, null, includeUnpublished);
|
|
616
|
assertEquals("Smerinthus is not in subtree", 0, numberOfTaxa);
|
|
617
|
numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
618
|
assertEquals("Atropos Agassiz and Atropos Oken expected as Synonyms", 2, numberOfTaxa);
|
|
619
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
620
|
assertEquals("The above accepted and synonyms expected", 5, numberOfTaxa);
|
|
621
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Aasfwerfwf fffe", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
622
|
assertEquals(0, numberOfTaxa);
|
|
623
|
|
|
624
|
classification = classificationDao.findByUuid(UUID_CLASSIFICATION2);
|
|
625
|
subtree = null;
|
|
626
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
627
|
assertEquals("Acherontia and 2 A. species expected", 3, numberOfTaxa);
|
|
628
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "S", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
629
|
assertEquals("Sphingidae expected", 1, numberOfTaxa);
|
|
630
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Smerinthus kindermannii", classification, subtree, MatchMode.EXACT, null, includeUnpublished);
|
|
631
|
assertEquals("Smerinthus is not in subtree", 0, numberOfTaxa);
|
|
632
|
numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
633
|
assertEquals("Atropos Agassiz and Atropos Oken expected as Synonyms", 2, numberOfTaxa);
|
|
634
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
635
|
assertEquals("The above accepted and synonyms expected", 5, numberOfTaxa);
|
|
636
|
numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Aasfwerfwf fffe", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
|
|
637
|
assertEquals(0, numberOfTaxa);
|
|
638
|
}
|
|
639
|
|
|
640
|
@Test
|
|
641
|
@DataSet
|
|
642
|
public void testRelatedTaxa() {
|
|
643
|
Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
|
|
644
|
assert taxon != null : "taxon must exist";
|
|
645
|
|
|
646
|
List<String> propertyPaths = new ArrayList<>();
|
|
647
|
propertyPaths.add("fromTaxon");
|
|
648
|
propertyPaths.add("fromTaxon.name");
|
|
649
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
650
|
orderHints.add(new OrderHint("relatedFrom.name.genusOrUninomial", SortOrder.ASCENDING));
|
|
651
|
orderHints.add(new OrderHint("relatedFrom.name.specificEpithet", SortOrder.ASCENDING));
|
|
652
|
orderHints.add(new OrderHint("relatedFrom.name.infraSpecificEpithet", SortOrder.ASCENDING));
|
|
653
|
|
|
654
|
long count = taxonDao.countTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
655
|
includeUnpublished, TaxonRelationship.Direction.relatedTo);
|
|
656
|
assertEquals("Count should return 8 (related taxa)", 8, count);
|
|
657
|
|
|
658
|
List<TaxonRelationship> relatedTaxa = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
659
|
includeUnpublished, null, null, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
660
|
assertNotNull("getRelatedTaxa should return a List",relatedTaxa);
|
|
661
|
assertEquals("getRelatedTaxa should return all 8 related taxa", 8, relatedTaxa.size());
|
|
662
|
assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate.isInitialized(relatedTaxa.get(0).getFromTaxon()));
|
|
663
|
assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate.isInitialized(relatedTaxa.get(0).getFromTaxon().getName()));
|
|
664
|
|
|
665
|
assertEquals("Acherontia should appear first in the list of related taxa", relatedTaxa.get(0).getFromTaxon().getTitleCache(), "Acherontia Laspeyres, 1809 sec. cate-sphingidae.org");
|
|
666
|
assertEquals("Sphingonaepiopsis should appear last in the list of related taxa", "Sphingonaepiopsis Wallengren, 1858 sec. cate-sphingidae.org", relatedTaxa.get(relatedTaxa.size()-1).getFromTaxon().getTitleCache());
|
|
667
|
}
|
|
668
|
|
|
669
|
@Test
|
|
670
|
@DataSet
|
|
671
|
public void testGetRelatedTaxaPaged() {
|
|
672
|
Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
|
|
673
|
assert taxon != null : "taxon must exist";
|
|
674
|
|
|
675
|
List<String> propertyPaths = new ArrayList<>();
|
|
676
|
propertyPaths.add("fromTaxon");
|
|
677
|
propertyPaths.add("fromTaxon.name");
|
|
678
|
|
|
679
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
680
|
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
|
|
681
|
|
|
682
|
int pageSize = 3;
|
|
683
|
List<TaxonRelationship> firstPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
684
|
includeUnpublished, pageSize, 0, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
685
|
List<TaxonRelationship> secondPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
686
|
includeUnpublished, pageSize, 1, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
687
|
List<TaxonRelationship> thirdPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
688
|
includeUnpublished, pageSize, 2, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
|
|
689
|
|
|
690
|
assertNotNull("getRelatedTaxa: 3, 0 should return a List",firstPage);
|
|
691
|
assertEquals("getRelatedTaxa: 3, 0 should return a List with 3 elements", pageSize,firstPage.size());
|
|
692
|
assertNotNull("getRelatedTaxa: 3, 1 should return a List",secondPage);
|
|
693
|
assertEquals("getRelatedTaxa: 3, 1 should return a List with 3 elements", pageSize, secondPage.size());
|
|
694
|
assertNotNull("getRelatedTaxa: 3, 2 should return a List",thirdPage);
|
|
695
|
assertEquals("getRelatedTaxa: 3, 2 should return a List with 2 elements", 2, thirdPage.size());
|
|
696
|
}
|
|
697
|
|
|
698
|
@Test
|
|
699
|
@DataSet
|
|
700
|
public void testCountSynonyms() {
|
|
701
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
702
|
assert taxon != null : "taxon must exist";
|
|
703
|
|
|
704
|
long numberOfRelatedSynonym = taxonDao.countSynonyms(taxon,null);
|
|
705
|
assertEquals("countSynonyms should return 3", 3, numberOfRelatedSynonym);
|
|
706
|
}
|
|
707
|
|
|
708
|
@Test
|
|
709
|
@DataSet
|
|
710
|
public void testGetSynonyms() {
|
|
711
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
712
|
assert taxon != null : "taxon must exist";
|
|
713
|
List<String> propertyPaths = new ArrayList<String>();
|
|
714
|
propertyPaths.add("synonym");
|
|
715
|
propertyPaths.add("synonym.name");
|
|
716
|
|
|
717
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
718
|
orderHints.add(new OrderHint("titleCache", SortOrder.ASCENDING));
|
|
719
|
|
|
720
|
List<Synonym> synonyms = taxonDao.getSynonyms(taxon, null, null, null,orderHints,propertyPaths);
|
|
721
|
|
|
722
|
assertNotNull("getSynonyms should return a List", synonyms);
|
|
723
|
assertEquals("getSynonyms should return 3 synonyms", 3, synonyms.size());
|
|
724
|
assertTrue("getSynonyms should return synonym objects with the synonym initialized", Hibernate.isInitialized(synonyms.get(0)));
|
|
725
|
}
|
|
726
|
|
|
727
|
@Test
|
|
728
|
@DataSet
|
|
729
|
public void testCountSynonymsByType() {
|
|
730
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
731
|
assert taxon != null : "taxon must exist";
|
|
732
|
|
|
733
|
long numberOfTaxonomicSynonyms = taxonDao.countSynonyms(taxon, SynonymType.HETEROTYPIC_SYNONYM_OF());
|
|
734
|
assertEquals("countSynonyms should return 4", 3, numberOfTaxonomicSynonyms);
|
|
735
|
}
|
|
736
|
|
|
737
|
@Test
|
|
738
|
@DataSet
|
|
739
|
public void testSynonymsByType() {
|
|
740
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
741
|
assert taxon != null : "taxon must exist";
|
|
742
|
|
|
743
|
List<Synonym> synonyms = taxonDao.getSynonyms(taxon, SynonymType.HETEROTYPIC_SYNONYM_OF(), null, null,null,null);
|
|
744
|
|
|
745
|
assertNotNull("getSynonyms should return a List", synonyms);
|
|
746
|
assertEquals("getSynonyms should return 4 Synonyms", 3, synonyms.size());
|
|
747
|
}
|
|
748
|
|
|
749
|
@Test
|
|
750
|
@DataSet
|
|
751
|
public void testPageSynonyms(){
|
|
752
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
753
|
assert taxon != null : "taxon must exist";
|
|
754
|
|
|
755
|
int pageSize = 2;
|
|
756
|
List<Synonym> firstPage = taxonDao.getSynonyms(taxon, null, pageSize, 0,null,null);
|
|
757
|
List<Synonym> secondPage = taxonDao.getSynonyms(taxon, null, pageSize, 1,null,null);
|
|
758
|
|
|
759
|
assertNotNull("getSynonyms: 2, 0 should return a List",firstPage);
|
|
760
|
assertEquals("getSynonyms: 2, 0 should return 2 synonyms", pageSize,firstPage.size());
|
|
761
|
assertNotNull("getSynonyms: 2, 1 should return a List",secondPage);
|
|
762
|
assertEquals("getSynonyms: 2, 1 should return 1 synonym", 1, secondPage.size());
|
|
763
|
}
|
|
764
|
|
|
765
|
@Test
|
|
766
|
@DataSet
|
|
767
|
public void testCountTaxonRelationships() {
|
|
768
|
long count = taxonDao.countTaxonRelationships(null);
|
|
769
|
assertEquals("There should be 11 relationships", 11, count);
|
|
770
|
|
|
771
|
Set<TaxonRelationshipType> types = new HashSet<>();
|
|
772
|
count = taxonDao.countTaxonRelationships(types);
|
|
773
|
assertEquals("Empty filter should return empty result", 0, count);
|
|
774
|
|
|
775
|
types.add(TaxonRelationshipType.CONGRUENT_TO());
|
|
776
|
count = taxonDao.countTaxonRelationships(types);
|
|
777
|
assertEquals("There should be no congruent relationship", 0, count);
|
|
778
|
|
|
779
|
types.add(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN());
|
|
780
|
count = taxonDao.countTaxonRelationships(types);
|
|
781
|
assertEquals("There should be 11 tax included relationships", 11, count);
|
|
782
|
}
|
|
783
|
|
|
784
|
@Test
|
|
785
|
@DataSet
|
|
786
|
public void testlistTaxonRelationships() {
|
|
787
|
List<TaxonRelationship> rels = taxonDao.getTaxonRelationships(null, null, null, null, null);
|
|
788
|
assertEquals("There should be 11 relationships", 11, rels.size());
|
|
789
|
|
|
790
|
rels = taxonDao.getTaxonRelationships(null, 2, 3, null, null);
|
|
791
|
assertEquals("There should be 11 relationships", 2, rels.size());
|
|
792
|
|
|
793
|
Set<TaxonRelationshipType> types = new HashSet<>();
|
|
794
|
rels = taxonDao.getTaxonRelationships(types, null, null, null, null);
|
|
795
|
assertEquals("Empty filter should return empty result", 0, rels.size());
|
|
796
|
|
|
797
|
types.add(TaxonRelationshipType.CONGRUENT_TO());
|
|
798
|
rels = taxonDao.getTaxonRelationships(types, null, null, null, null);
|
|
799
|
assertEquals("There should be no congruent relationship", 0, rels.size());
|
|
800
|
|
|
801
|
types.add(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN());
|
|
802
|
rels = taxonDao.getTaxonRelationships(types, null, null, null, null);
|
|
803
|
assertEquals("There should be 11 tax included relationships", 11, rels.size());
|
|
804
|
}
|
|
805
|
|
|
806
|
@Test
|
|
807
|
@DataSet("TaxonNodeDaoHibernateImplTest.xml")
|
|
808
|
public void testListAcceptedTaxaFor() {
|
|
809
|
UUID acheontitia_ciprosus = UUID.fromString("3ef145f7-bd92-4a64-8afd-2b8203e00e02");
|
|
810
|
|
|
811
|
Synonym synonym = (Synonym)taxonDao.findByUuid(acheontitia_ciprosus);
|
|
812
|
assertNotNull("synonym must exist", synonym);
|
|
813
|
|
|
814
|
Taxon taxon = taxonDao.acceptedTaxonFor(synonym, null, null);
|
|
815
|
assertNotNull("listAcceptedTaxaFor should return a taxon", taxon);
|
|
816
|
|
|
817
|
Classification classification = classificationDao.load(classificationUuid);
|
|
818
|
assertNotNull("classification must exist", classification);
|
|
819
|
|
|
820
|
taxon = taxonDao.acceptedTaxonFor(synonym, classification, null);
|
|
821
|
assertNull("listAcceptedTaxaFor should return not taxon due to classification filter", taxon);
|
|
822
|
}
|
|
823
|
|
|
824
|
|
|
825
|
@Test
|
|
826
|
@DataSet
|
|
827
|
public void testGetTaxonMatchingUninomial() {
|
|
828
|
@SuppressWarnings("rawtypes")
|
|
829
|
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*","*",null,null,null);
|
|
830
|
|
|
831
|
assertNotNull("findTaxaByName should return a List", result);
|
|
832
|
assertEquals("findTaxaByName should return two Taxa",2,result.size());
|
|
833
|
assertEquals("findTaxaByName should return a Taxon with id 5",5,result.get(0).getId());
|
|
834
|
}
|
|
835
|
|
|
836
|
@Test
|
|
837
|
@DataSet
|
|
838
|
public void testGetTaxonMatchingSpeciesBinomial() {
|
|
839
|
@SuppressWarnings("rawtypes")
|
|
840
|
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", null, "kindermannii", null,"*",null,null,null);
|
|
841
|
|
|
842
|
assertNotNull("findTaxaByName should return a List", result);
|
|
843
|
assertEquals("findTaxaByName should return one Taxon",1,result.size());
|
|
844
|
assertEquals("findTaxaByName should return a Taxon with id 8",8,result.get(0).getId());
|
|
845
|
}
|
|
846
|
|
|
847
|
@Test
|
|
848
|
@DataSet
|
|
849
|
public void testGetTaxonMatchingTrinomial() {
|
|
850
|
@SuppressWarnings("rawtypes")
|
|
851
|
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis","*",null,null,null);
|
|
852
|
|
|
853
|
assertNotNull("findTaxaByName should return a List", result);
|
|
854
|
assertEquals("findTaxaByName should return one Taxon",1,result.size());
|
|
855
|
assertEquals("findTaxaByName should return a Taxon with id 38",38,result.get(0).getId());
|
|
856
|
}
|
|
857
|
|
|
858
|
@Test
|
|
859
|
@DataSet
|
|
860
|
public void testNegativeMatch() {
|
|
861
|
@SuppressWarnings("rawtypes")
|
|
862
|
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null,null);
|
|
863
|
|
|
864
|
assertNotNull("findTaxaByName should return a List", result);
|
|
865
|
assertTrue("findTaxaByName should return an empty List",result.isEmpty());
|
|
866
|
}
|
|
867
|
|
|
868
|
@Test
|
|
869
|
@DataSet
|
|
870
|
public void testCountAllTaxa() {
|
|
871
|
long numberOfTaxa = taxonDao.count(Taxon.class);
|
|
872
|
assertEquals("count should return 14 taxa", 14, numberOfTaxa);
|
|
873
|
}
|
|
874
|
|
|
875
|
@Test
|
|
876
|
@DataSet
|
|
877
|
public void testListAllTaxa() {
|
|
878
|
List<Taxon> taxa = taxonDao.list(Taxon.class,100, 0);
|
|
879
|
assertNotNull("list should return a List", taxa);
|
|
880
|
assertEquals("list should return 14 taxa", 14, taxa.size());
|
|
881
|
}
|
|
882
|
|
|
883
|
@Test
|
|
884
|
@DataSet
|
|
885
|
// @ExpectedDataSet
|
|
886
|
public void testDelete() {
|
|
887
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
888
|
assert taxon != null : "taxon must exist";
|
|
889
|
taxonDao.delete(taxon);
|
|
890
|
taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
891
|
assert taxon == null : "taxon must not exist";
|
|
892
|
setComplete();
|
|
893
|
endTransaction();
|
|
894
|
// try {
|
|
895
|
// printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
|
|
896
|
// } catch (FileNotFoundException e) {
|
|
897
|
// e.printStackTrace();
|
|
898
|
// }
|
|
899
|
}
|
|
900
|
|
|
901
|
@Test
|
|
902
|
@DataSet
|
|
903
|
@ExpectedDataSet("TaxonDaoHibernateImplTest.testDelete-result.xml")
|
|
904
|
public void testDeleteWithMarker() {
|
|
905
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
906
|
taxon.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), true));
|
|
907
|
taxonDao.save(taxon);
|
|
908
|
assert taxon != null : "taxon must exist";
|
|
909
|
|
|
910
|
taxonDao.delete(taxon);
|
|
911
|
commitAndStartNewTransaction(null);
|
|
912
|
taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
913
|
assert taxon == null : "taxon must not exist";
|
|
914
|
setComplete();
|
|
915
|
endTransaction();
|
|
916
|
// try {
|
|
917
|
// printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
|
|
918
|
// } catch (FileNotFoundException e) {
|
|
919
|
// e.printStackTrace();
|
|
920
|
// }
|
|
921
|
}
|
|
922
|
|
|
923
|
@Test
|
|
924
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
925
|
public void testFindDeleted() {
|
|
926
|
TaxonBase<?> taxon = taxonDao.findByUuid(acherontia);
|
|
927
|
assertNull("findByUuid should return null in this view", taxon);
|
|
928
|
assertFalse("exist should return false in this view",taxonDao.exists(acherontia));
|
|
929
|
}
|
|
930
|
|
|
931
|
@Test
|
|
932
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
933
|
public void testFindDeletedInPreviousView() {
|
|
934
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
935
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
|
|
936
|
assertNotNull("findByUuid should return a taxon in this view",taxon);
|
|
937
|
assertTrue("exists should return true in this view", taxonDao.exists(acherontia));
|
|
938
|
|
|
939
|
try{
|
|
940
|
assertEquals("There should be 3 relations to this taxon in this view",3,taxon.getRelationsToThisTaxon().size());
|
|
941
|
} catch(Exception e) {
|
|
942
|
fail("We should not experience any problems initializing proxies with envers");
|
|
943
|
}
|
|
944
|
}
|
|
945
|
|
|
946
|
@Test
|
|
947
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
948
|
public void testGetAuditEvents() {
|
|
949
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
950
|
assert taxon != null : "taxon cannot be null";
|
|
951
|
|
|
952
|
List<String> propertyPaths = new ArrayList<>();
|
|
953
|
propertyPaths.add("name");
|
|
954
|
propertyPaths.add("createdBy");
|
|
955
|
propertyPaths.add("updatedBy");
|
|
956
|
|
|
957
|
@SuppressWarnings("rawtypes")
|
|
958
|
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(taxon, null,null,null,propertyPaths);
|
|
959
|
assertNotNull("getAuditEvents should return a list",auditEvents);
|
|
960
|
assertFalse("the list should not be empty",auditEvents.isEmpty());
|
|
961
|
assertEquals("There should be two AuditEventRecords in the list",2, auditEvents.size());
|
|
962
|
}
|
|
963
|
|
|
964
|
@Test
|
|
965
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
966
|
public void testGetAuditEventsFromNow() {
|
|
967
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
968
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
969
|
assert taxon != null : "taxon cannot be null";
|
|
970
|
|
|
971
|
@SuppressWarnings("rawtypes")
|
|
972
|
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(taxon, null,null,AuditEventSort.FORWARDS,null);
|
|
973
|
assertNotNull("getAuditEvents should return a list",auditEvents);
|
|
974
|
assertFalse("the list should not be empty",auditEvents.isEmpty());
|
|
975
|
assertEquals("There should be one audit event in the list",1,auditEvents.size());
|
|
976
|
}
|
|
977
|
|
|
978
|
@Test
|
|
979
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
980
|
public void testCountAuditEvents() {
|
|
981
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
982
|
assert taxon != null : "taxon cannot be null";
|
|
983
|
|
|
984
|
long numberOfAuditEvents = taxonDao.countAuditEvents(taxon, null);
|
|
985
|
assertEquals("countAuditEvents should return 2",numberOfAuditEvents,2);
|
|
986
|
}
|
|
987
|
|
|
988
|
@Test
|
|
989
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
990
|
public void getPreviousAuditEvent() {
|
|
991
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
992
|
assert taxon != null : "taxon cannot be null";
|
|
993
|
|
|
994
|
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getPreviousAuditEvent(taxon);
|
|
995
|
assertNotNull("getPreviousAuditEvent should not return null as there is at least one audit event prior to the current one",auditEvent);
|
|
996
|
}
|
|
997
|
|
|
998
|
@Test
|
|
999
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
1000
|
public void getPreviousAuditEventAtBeginning() {
|
|
1001
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
1002
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
1003
|
assert taxon != null : "taxon cannot be null";
|
|
1004
|
|
|
1005
|
@SuppressWarnings("rawtypes")
|
|
1006
|
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getPreviousAuditEvent(taxon);
|
|
1007
|
assertNull("getPreviousAuditEvent should return null if we're at the first audit event anyway",auditEvent);
|
|
1008
|
}
|
|
1009
|
|
|
1010
|
@Test
|
|
1011
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
1012
|
public void getNextAuditEvent() {
|
|
1013
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
1014
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
1015
|
assert taxon != null : "taxon cannot be null";
|
|
1016
|
|
|
1017
|
@SuppressWarnings("rawtypes")
|
|
1018
|
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getNextAuditEvent(taxon);
|
|
1019
|
assertNotNull("getNextAuditEvent should not return null as there is at least one audit event after the current one",auditEvent);
|
|
1020
|
}
|
|
1021
|
|
|
1022
|
@Test
|
|
1023
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
1024
|
public void getNextAuditEventAtEnd() {
|
|
1025
|
AuditEventContextHolder.getContext().setAuditEvent(mostRecentAuditEvent);
|
|
1026
|
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
|
|
1027
|
assert taxon != null : "taxon cannot be null";
|
|
1028
|
|
|
1029
|
@SuppressWarnings("rawtypes")
|
|
1030
|
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getNextAuditEvent(taxon);
|
|
1031
|
assertNull("getNextAuditEvent should return null as there no more audit events after the current one",auditEvent);
|
|
1032
|
}
|
|
1033
|
|
|
1034
|
@Test
|
|
1035
|
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
|
|
1036
|
public void testFind() {
|
|
1037
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
|
|
1038
|
assert taxon != null : "taxon cannot be null";
|
|
1039
|
|
|
1040
|
assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon.getRelationsToThisTaxon().size());
|
|
1041
|
}
|
|
1042
|
|
|
1043
|
@Test
|
|
1044
|
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
|
|
1045
|
public void testFindInPreviousView() {
|
|
1046
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
1047
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
|
|
1048
|
assert taxon != null : "taxon cannot be null";
|
|
1049
|
|
|
1050
|
assertTrue("getRelationsToThisTaxon should contain 0 TaxonRelationship in this view",taxon.getRelationsToThisTaxon().isEmpty());
|
|
1051
|
}
|
|
1052
|
|
|
1053
|
@Test
|
|
1054
|
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
|
|
1055
|
public void testGetRelations() {
|
|
1056
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
|
|
1057
|
assert taxon != null : "taxon cannot be null";
|
|
1058
|
|
|
1059
|
List<String> propertyPaths = new ArrayList<>();
|
|
1060
|
propertyPaths.add("fromTaxon");
|
|
1061
|
propertyPaths.add("fromTaxon.name");
|
|
1062
|
|
|
1063
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
1064
|
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
|
|
1065
|
|
|
1066
|
List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
1067
|
includeUnpublished, null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
|
1068
|
assertNotNull("getRelatedTaxa should return a list", taxonRelations);
|
|
1069
|
assertEquals("there should be one TaxonRelationship in the list in the current view",1,taxonRelations.size());
|
|
1070
|
assertTrue("TaxonRelationship.relatedFrom should be initialized",Hibernate.isInitialized(taxonRelations.get(0).getFromTaxon()));
|
|
1071
|
assertTrue("TaxonRelationship.relatedFrom.name should be initialized",Hibernate.isInitialized(taxonRelations.get(0).getFromTaxon().getName()));
|
|
1072
|
}
|
|
1073
|
|
|
1074
|
@Test
|
|
1075
|
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
|
|
1076
|
public void testCountRelations() {
|
|
1077
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
|
|
1078
|
assert taxon != null : "taxon cannot be null";
|
|
1079
|
assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao.countTaxonRelationships(
|
|
1080
|
taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
1081
|
includeUnpublished, TaxonRelationship.Direction.relatedTo));
|
|
1082
|
}
|
|
1083
|
|
|
1084
|
@Test
|
|
1085
|
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
|
|
1086
|
public void testGetRelationsInPreviousView() {
|
|
1087
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
1088
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
|
|
1089
|
assert taxon != null : "taxon cannot be null";
|
|
1090
|
|
|
1091
|
List<String> propertyPaths = new ArrayList<String>();
|
|
1092
|
propertyPaths.add("relatedFrom");
|
|
1093
|
propertyPaths.add("relatedFrom.name");
|
|
1094
|
|
|
1095
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
1096
|
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
|
|
1097
|
|
|
1098
|
List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
1099
|
includeUnpublished, null, null, orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
|
|
1100
|
assertNotNull("getRelatedTaxa should return a list",taxonRelations);
|
|
1101
|
assertTrue("there should be no TaxonRelationships in the list in the prior view", taxonRelations.isEmpty());
|
|
1102
|
}
|
|
1103
|
|
|
1104
|
@Test
|
|
1105
|
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
|
|
1106
|
public void testCountRelationsInPreviousView() {
|
|
1107
|
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
|
|
1108
|
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
|
|
1109
|
assert taxon != null : "taxon cannot be null";
|
|
1110
|
assertEquals("countRelatedTaxa should return 0 in the current view",0,
|
|
1111
|
taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
|
|
1112
|
includeUnpublished, TaxonRelationship.Direction.relatedTo));
|
|
1113
|
}
|
|
1114
|
|
|
1115
|
@Test
|
|
1116
|
@DataSet
|
|
1117
|
public void testGroupTaxa() {
|
|
1118
|
List<Grouping> groups = new ArrayList<>();
|
|
1119
|
groups.add(new GroupByCount("count",SortOrder.DESCENDING));
|
|
1120
|
groups.add(new Grouping("name.genusOrUninomial", "genus", "n", SortOrder.ASCENDING));
|
|
1121
|
List<Object[]> results = taxonDao.group(null, null, null, groups,null);
|
|
1122
|
if(logger.isTraceEnabled()){
|
|
1123
|
System.out.println("count\tname.genuOrUninomial");
|
|
1124
|
for(Object[] result : results) {
|
|
1125
|
System.out.println(result[0] + "\t" + result[1]);
|
|
1126
|
}
|
|
1127
|
}
|
|
1128
|
}
|
|
1129
|
|
|
1130
|
@Test
|
|
1131
|
@DataSet
|
|
1132
|
public void testGroupTaxaByClass() {
|
|
1133
|
List<Grouping> groups = new ArrayList<>();
|
|
1134
|
groups.add(new GroupByCount("count",SortOrder.DESCENDING));
|
|
1135
|
groups.add(new Grouping("class", "class",null, SortOrder.ASCENDING));
|
|
1136
|
List<Object[]> results = taxonDao.group(null, null, null, groups,null);
|
|
1137
|
if(logger.isTraceEnabled()){
|
|
1138
|
System.out.println("count\tclass");
|
|
1139
|
for(Object[] result : results) {
|
|
1140
|
System.out.println(result[0] + "\t" + result[1]);
|
|
1141
|
}
|
|
1142
|
}
|
|
1143
|
}
|
|
1144
|
|
|
1145
|
@Test
|
|
1146
|
@DataSet
|
|
1147
|
public void testNativeSQLOrder() {
|
|
1148
|
List<OrderHint> orderHints = new ArrayList<>();
|
|
1149
|
orderHints.add(new NativeSqlOrderHint("case when {alias}.titleCache like 'C%' then 0 else 1 end",SortOrder.ASCENDING));
|
|
1150
|
|
|
1151
|
@SuppressWarnings("rawtypes")
|
|
1152
|
List<TaxonBase> results = taxonDao.list(null, null, orderHints);
|
|
1153
|
if(logger.isTraceEnabled()){
|
|
1154
|
System.out.println("native SQL order");
|
|
1155
|
for(TaxonBase<?> result : results) {
|
|
1156
|
System.out.println(result.getTitleCache());
|
|
1157
|
}
|
|
1158
|
}
|
|
1159
|
}
|
|
1160
|
|
|
1161
|
@Test
|
|
1162
|
@DataSet
|
|
1163
|
public void testGroupByDateTaxa() {
|
|
1164
|
List<Grouping> groups = new ArrayList<>();
|
|
1165
|
groups.add(new GroupByCount("count",null));
|
|
1166
|
groups.add(new GroupByDate("created", "dateGroup", SortOrder.ASCENDING, GroupByDate.Resolution.MONTH));
|
|
1167
|
List<Object[]> results = taxonDao.group(null, null, null, groups,null);
|
|
1168
|
if(logger.isTraceEnabled()){
|
|
1169
|
System.out.println("count\tyear\tmonth");
|
|
1170
|
for(Object[] result : results) {
|
|
1171
|
System.out.println(result[0] + "\t" + result[1] + "\t" + result[2]);
|
|
1172
|
}
|
|
1173
|
}
|
|
1174
|
}
|
|
1175
|
|
|
1176
|
|
|
1177
|
|
|
1178
|
|
|
1179
|
@Test
|
|
1180
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
1181
|
//NOTE: There is a problem with loading AuditEvents if this test runs
|
|
1182
|
//stand alone or as first (one of the first) in the test suite. For some reason
|
|
1183
|
//the AuditEvent records from the @DataSet are not inserted into the database then,
|
|
1184
|
//while those inserted by the terms dataset are inserted as well as a completely new one.
|
|
1185
|
//This problem for some reason does not happen if not running at first place
|
|
1186
|
public void testGetAuditEventsByTypeWithRestrictions() {
|
|
1187
|
commitAndStartNewTransaction(new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
|
|
1188
|
|
|
1189
|
List<String> propertyPaths = new ArrayList<>();
|
|
1190
|
propertyPaths.add("name");
|
|
1191
|
propertyPaths.add("createdBy");
|
|
1192
|
propertyPaths.add("updatedBy");
|
|
1193
|
|
|
1194
|
List<AuditCriterion> criteria = new ArrayList<>();
|
|
1195
|
criteria.add(AuditEntity.property("lsid_lsid").isNotNull());
|
|
1196
|
|
|
1197
|
long count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
|
|
1198
|
|
|
1199
|
@SuppressWarnings("rawtypes")
|
|
1200
|
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(TaxonBase.class, previousAuditEvent, mostRecentAuditEvent, criteria,null, null, AuditEventSort.FORWARDS, propertyPaths);
|
|
1201
|
assertNotNull("getAuditEvents should return a list",auditEvents);
|
|
1202
|
assertFalse("the list should not be empty",auditEvents.isEmpty());
|
|
1203
|
assertEquals("There should be one AuditEventRecord in the list",1, auditEvents.size());
|
|
1204
|
}
|
|
1205
|
|
|
1206
|
|
|
1207
|
@Test
|
|
1208
|
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
|
|
1209
|
// @DataSets({ //for testing only
|
|
1210
|
// @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml"),
|
|
1211
|
// @DataSet("TaxonDaoHibernateImplTest.testFindDeletedAuditEvents.xml")
|
|
1212
|
// })
|
|
1213
|
//NOTE: There is a problem with loading AuditEvents if this test runs
|
|
1214
|
//stand alone or as first (one of the first) in the test suite. For some reason
|
|
1215
|
//the AuditEvent records from the @DataSet are not inserted into the database then,
|
|
1216
|
//while those inserted by the terms dataset are inserted as well as a completely new one.
|
|
1217
|
//This problem for some reason does not happen if not running at first place
|
|
1218
|
public void testGetAuditEventsByTypeWithNoRestrictions() {
|
|
1219
|
// printDataSet(System.out, new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
|
|
1220
|
commitAndStartNewTransaction(new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
|
|
1221
|
|
|
1222
|
List<String> propertyPaths = new ArrayList<>();
|
|
1223
|
propertyPaths.add("name");
|
|
1224
|
propertyPaths.add("createdBy");
|
|
1225
|
propertyPaths.add("updatedBy");
|
|
1226
|
long count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
|
|
1227
|
@SuppressWarnings("rawtypes")
|
|
1228
|
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(TaxonBase.class, previousAuditEvent, mostRecentAuditEvent, null,null, null, AuditEventSort.FORWARDS, propertyPaths);
|
|
1229
|
assertNotNull("getAuditEvents should return a list", auditEvents);
|
|
1230
|
assertFalse("the list should not be empty", auditEvents.isEmpty());
|
|
1231
|
assertEquals("There should be thirty eight AuditEventRecords in the list", 2, auditEvents.size());
|
|
1232
|
}
|
|
1233
|
|
|
1234
|
|
|
1235
|
@Test
|
|
1236
|
@DataSet("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
|
|
1237
|
public void testGetCommonName(){
|
|
1238
|
List<Taxon> commonNameResults = taxonDao.getTaxaByCommonName("common%", null,
|
|
1239
|
MatchMode.BEGINNING, null, null, null, null);
|
|
1240
|
|
|
1241
|
assertNotNull("getTaxaByCommonName should return a list", commonNameResults);
|
|
1242
|
assertFalse("the list should not be empty", commonNameResults.isEmpty());
|
|
1243
|
assertEquals("There should be two taxa with common name", 2,commonNameResults.size());
|
|
1244
|
|
|
1245
|
List<UuidAndTitleCache<Taxon>> list = taxonDao.getTaxaByCommonNameForEditor(
|
|
1246
|
"common%", null, MatchMode.BEGINNING, null);
|
|
1247
|
|
|
1248
|
assertNotNull("getTaxaByCommonName should return a list", list);
|
|
1249
|
assertFalse("the list should not be empty", list.isEmpty());
|
|
1250
|
assertEquals("There should be two Taxon with common name", 2,list.size());
|
|
1251
|
|
|
1252
|
}
|
|
1253
|
|
|
1254
|
@Test
|
|
1255
|
@DataSet
|
|
1256
|
public void testGetTitleCache(){
|
|
1257
|
UUID uuid = UUID.fromString("7b8b5cb3-37ba-4dba-91ac-4c6ffd6ac331");
|
|
1258
|
String titleCache = taxonDao.getTitleCache(uuid, false);
|
|
1259
|
Assert.assertEquals("Acherontia styx Westwood, 1847 sec. cate-sphingidae.org", titleCache);
|
|
1260
|
titleCache = taxonDao.getTitleCache(uuid, true);
|
|
1261
|
Assert.assertEquals("Acherontia styxx Westwood, 1847 sec. cate-sphingidae.org", titleCache);
|
|
1262
|
}
|
|
1263
|
|
|
1264
|
|
|
1265
|
@Test
|
|
1266
|
@DataSet("TaxonDaoHibernateImplTest.testPropertyPath.xml")
|
|
1267
|
public void testPropertyPath(){
|
|
1268
|
//Test that BeanInitializer also works on HiberanteProxys
|
|
1269
|
Classification c = classificationDao.load(UUID.fromString("4bceea53-893f-4685-8c63-6dcec6e85ab1"));
|
|
1270
|
TaxonNode singleNode = c.getRootNode().getChildNodes().iterator().next();
|
|
1271
|
Taxon taxonProxy = singleNode.getTaxon();
|
|
1272
|
Assert.assertTrue("Object to test should be a proxy ", taxonProxy instanceof HibernateProxy);
|
|
1273
|
|
|
1274
|
List<String> propertyPaths = new ArrayList<>();
|
|
1275
|
propertyPaths.add("taxonNodes");
|
|
1276
|
Taxon taxon = (Taxon)this.taxonDao.load(
|
|
1277
|
UUID.fromString("4a5bc930-844f-45ec-aea8-dd155e1ab25f"),
|
|
1278
|
propertyPaths);
|
|
1279
|
Assert.assertSame("Returned object should be the same proxy to assure that we ran initialization on this proxy", taxonProxy, taxon);
|
|
1280
|
}
|
|
1281
|
|
|
1282
|
|
|
1283
|
/**
|
|
1284
|
* {@inheritDoc}
|
|
1285
|
*/
|
|
1286
|
@Override
|
|
1287
|
// @Test
|
|
1288
|
public void createTestDataSet() throws FileNotFoundException {
|
|
1289
|
// Classification classification = Classification.NewInstance("Test");
|
|
1290
|
// BotanicalName TaxonName = null;
|
|
1291
|
// Reference sec = null;
|
|
1292
|
// Taxon taxon = Taxon.NewInstance(taxonName, sec);
|
|
1293
|
// classification.addChildTaxon(taxon, sec, null);
|
|
1294
|
//
|
|
1295
|
// classificationDao.save(classification);
|
|
1296
|
// this.commitAndStartNewTransaction(null);
|
|
1297
|
//
|
|
1298
|
// writeDbUnitDataSetFile(new String[] {
|
|
1299
|
// "CLASSIFICATION", "TAXONNAME",
|
|
1300
|
// "REFERENCE","TAXONNODE",
|
|
1301
|
// "TAXONBASE","LANGUAGESTRING",
|
|
1302
|
// "HIBERNATE_SEQUENCES" // IMPORTANT!!!
|
|
1303
|
// },
|
|
1304
|
// "testPropertyPath" );
|
|
1305
|
}
|
|
1306
|
|
|
1307
|
}
|