import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertSame;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import java.io.FileNotFoundException;
-import java.io.FileOutputStream;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import java.util.UUID;
-import org.apache.log4j.Level;
import org.hibernate.Hibernate;
import org.hibernate.envers.query.AuditEntity;
import org.hibernate.envers.query.criteria.AuditCriterion;
import org.unitils.dbunit.annotation.ExpectedDataSet;
import org.unitils.spring.annotation.SpringBeanByType;
-import eu.etaxonomy.cdm.hibernate.HibernateProxyHelper;
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
import eu.etaxonomy.cdm.model.common.Marker;
import eu.etaxonomy.cdm.model.common.MarkerType;
import eu.etaxonomy.cdm.model.location.NamedArea;
-import eu.etaxonomy.cdm.model.name.NonViralName;
-import eu.etaxonomy.cdm.model.name.Rank;
-import eu.etaxonomy.cdm.model.name.TaxonNameBase;
+import eu.etaxonomy.cdm.model.name.TaxonName;
import eu.etaxonomy.cdm.model.reference.Reference;
import eu.etaxonomy.cdm.model.taxon.Classification;
import eu.etaxonomy.cdm.model.taxon.Synonym;
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationship;
-import eu.etaxonomy.cdm.model.taxon.SynonymRelationshipType;
+import eu.etaxonomy.cdm.model.taxon.SynonymType;
import eu.etaxonomy.cdm.model.taxon.Taxon;
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
import eu.etaxonomy.cdm.persistence.dao.reference.IReferenceDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.IClassificationDao;
import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonDao;
+import eu.etaxonomy.cdm.persistence.dao.taxon.ITaxonNodeDao;
import eu.etaxonomy.cdm.persistence.dto.UuidAndTitleCache;
-import eu.etaxonomy.cdm.persistence.fetch.CdmFetch;
import eu.etaxonomy.cdm.persistence.query.GroupByCount;
import eu.etaxonomy.cdm.persistence.query.GroupByDate;
import eu.etaxonomy.cdm.persistence.query.Grouping;
/**
* @author a.mueller
* @author ben.clark
- *
*/
public class TaxonDaoHibernateImplTest extends CdmTransactionalIntegrationTest {
@SpringBeanByType
private ITaxonDao taxonDao;
+ @SpringBeanByType
+ private ITaxonNodeDao taxonNodeDao;
+
@SpringBeanByType
private IClassificationDao classificationDao;
private IReferenceDao referenceDao;
@SpringBeanByType
- IDefinedTermDao definedTermDao;
-
- private UUID uuid;
- private UUID sphingidae;
- private UUID acherontia;
- private UUID mimas;
- private UUID rethera;
- private UUID retheraSecCdmtest;
- private UUID atroposAgassiz; // a Synonym
- private UUID atroposLeach; // a Synonym
- private UUID acherontiaLachesis;
+ private IDefinedTermDao definedTermDao;
+
+ private UUID uuid = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
+ private UUID sphingidae = UUID.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9");
+ private UUID acherontia = UUID.fromString("c5cc8674-4242-49a4-aada-72d63194f5fa");
+ private UUID rethera = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
+ private UUID retheraSecCdmtest = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
+ private UUID atroposAgassiz = UUID.fromString("d75b2e3d-7394-4ada-b6a5-93175b8751c1"); // a Synonym
+ private UUID atroposOken = UUID.fromString("6bfedf25-6dbc-4d5c-9d56-84f9052f3b2a"); // a Synonym
+ private UUID atroposLeach = UUID.fromString("3da4ab34-6c50-4586-801e-732615899b07"); // a Synonym
+ private UUID acherontiaLachesis = UUID.fromString("b04cc9cb-2b4a-4cc4-a94a-3c93a2158b06");
+ private UUID aus = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
+
+ private UUID UUID_ACHERONTIA_NODE = UUID.fromString("56b10cf0-9522-407e-9f90-0c2dba263c94");
+ private UUID UUID_CLASSIFICATION2 = UUID.fromString("a71467a6-74dc-4148-9530-484628a5ab0e");
private AuditEvent previousAuditEvent;
private AuditEvent mostRecentAuditEvent;
private UUID northernAmericaUuid;
private UUID southernAmericaUuid;
- private UUID antarcticaUuid;
private UUID classificationUuid;
+ private boolean includeUnpublished = true;
+ private boolean NO_UNPUBLISHED = false;
+
+ private static final boolean doTaxa = true;
+ private static final boolean noTaxa = false;
+ private static final boolean doSynonyms = true;
+ private static final boolean noSynonyms = false;
+ private static final boolean doMisapplied = true;
+ private static final boolean noMisapplied = false;
+ private static final boolean doCommonNames = true;
+ private static final boolean noCommonNames = false;
+
+
+
+ @SuppressWarnings("unused")
private static final String[] TABLE_NAMES = new String[] {
- "HOMOTYPICALGROUP", "HOMOTYPICALGROUP_AUD", "REFERENCE", "REFERENCE_AUD", "SYNONYMRELATIONSHIP", "SYNONYMRELATIONSHIP_AUD", "TAXONBASE", "TAXONBASE_AUD"
- , "TAXONNAMEBASE", "TAXONNAMEBASE_AUD", "TAXONRELATIONSHIP", "TAXONRELATIONSHIP_AUD" };
+ "HOMOTYPICALGROUP", "HOMOTYPICALGROUP_AUD", "REFERENCE", "REFERENCE_AUD", "TAXONBASE", "TAXONBASE_AUD"
+ , "TAXONNAME", "TAXONNAME_AUD", "TAXONRELATIONSHIP", "TAXONRELATIONSHIP_AUD" };
@Before
public void setUp() {
- uuid = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
- sphingidae = UUID.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9");
- acherontia = UUID.fromString("c5cc8674-4242-49a4-aada-72d63194f5fa");
- acherontiaLachesis = UUID.fromString("b04cc9cb-2b4a-4cc4-a94a-3c93a2158b06");
- atroposAgassiz = UUID.fromString("d75b2e3d-7394-4ada-b6a5-93175b8751c1");
- atroposLeach = UUID.fromString("3da4ab34-6c50-4586-801e-732615899b07");
- rethera = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
- retheraSecCdmtest = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
- mimas = UUID.fromString("900052b7-b69c-4e26-a8f0-01c215214c40");
previousAuditEvent = new AuditEvent();
previousAuditEvent.setRevisionNumber(1025);
northernAmericaUuid = UUID.fromString("2757e726-d897-4546-93bd-7951d203bf6f");
southernAmericaUuid = UUID.fromString("6310b3ba-96f4-4855-bb5b-326e7af188ea");
- antarcticaUuid = UUID.fromString("791b3aa0-54dd-4bed-9b68-56b4680aad0c");
classificationUuid = UUID.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9");
+ includeUnpublished = true;
}
@After
assertNotNull("Instance of IReferenceDao expected",referenceDao);
}
- /**
- * Test method for
- * {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference)}
- * .
- */
@Test
@DataSet
- public void testGetRootTaxa() {
- Reference<?> sec1 = referenceDao.findById(1);
- assert sec1 != null : "sec1 must exist";
- Reference<?> sec2 = referenceDao.findById(2);
- assert sec2 != null : "sec2 must exist";
-
- List<Taxon> rootTaxa = taxonDao.getRootTaxa(sec1);
- assertNotNull("getRootTaxa should return a List", rootTaxa);
- assertFalse("The list should not be empty", rootTaxa.isEmpty());
- assertEquals("There should be one root taxon", 1, rootTaxa.size());
-
- rootTaxa = taxonDao.getRootTaxa(sec1, CdmFetch.FETCH_CHILDTAXA(), true, false);
- assertNotNull("getRootTaxa should return a List", rootTaxa);
- assertFalse("The list should not be empty", rootTaxa.isEmpty());
- assertEquals("There should be one root taxon", 1, rootTaxa.size());
-
- rootTaxa = taxonDao.getRootTaxa(Rank.GENUS(), sec1, CdmFetch.FETCH_CHILDTAXA(), true, false, null);
- assertNotNull("getRootTaxa should return a List", rootTaxa);
- assertFalse("The list should not be empty", rootTaxa.isEmpty());
- assertEquals("There should be one root taxon", 1, rootTaxa.size());
-
- rootTaxa = taxonDao.getRootTaxa(Rank.FAMILY(), sec2, CdmFetch.FETCH_CHILDTAXA(), true, false, null);
- if (logger.isDebugEnabled()) {
- logger.debug("Root taxa rank Family (" + rootTaxa.size() + "):");
- for (Taxon taxon : rootTaxa) {
- logger.debug(taxon.getTitleCache());
- }
- }
- assertEquals("There should be one root taxon rank Family", 1, rootTaxa.size());
- rootTaxa = taxonDao.getRootTaxa(Rank.GENUS(), sec2, CdmFetch.FETCH_CHILDTAXA(), true, false, null);
- assertNotNull("getRootTaxa should return a List", rootTaxa);
- assertFalse("The list should not be empty", rootTaxa.isEmpty());
- if (logger.isDebugEnabled()) {
- logger.debug("Root taxa rank Genus (" + rootTaxa.size() + "):");
- for (Taxon taxon : rootTaxa) {
- logger.debug(taxon.getTitleCache());
- }
- }
- assertEquals("There should be 22 root taxa rank Genus", 22, rootTaxa.size());
+ public void testGetTaxaByName() {
- rootTaxa = taxonDao.getRootTaxa(Rank.SPECIES(), sec2, CdmFetch.FETCH_CHILDTAXA(), true, false, null);
- if (logger.isDebugEnabled()) {
- logger.debug("Root taxa rank Species (" + rootTaxa.size() + "):");
- for (Taxon taxon : rootTaxa) {
- logger.debug(taxon.getTitleCache());
- }
- }
- assertEquals("There should be 4 root taxa rank Species", 3, rootTaxa.size());
- }
+ includeUnpublished= true;
+ boolean accepted = true;
- /**
- * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
- */
- @Test
- @DataSet
- public void testGetTaxaByName() {
- Reference<?> sec = referenceDao.findById(1);
+ Reference sec = referenceDao.findById(1);
assert sec != null : "sec must exist";
- List<TaxonBase> results = taxonDao.getTaxaByName("Aus", sec);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> results = taxonDao.getTaxaByName("Aus", includeUnpublished, sec);
assertNotNull("getTaxaByName should return a List", results);
//assertFalse("The list should not be empty", results.isEmpty());
- assertTrue(results.size() == 1);
+ assertEquals(1, results.size());
- results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, true, null, null);
+ results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, accepted, includeUnpublished, null, null);
assertNotNull("getTaxaByName should return a List", results);
- int numberOfTaxaByName_A = 9;
+ int numberOfTaxaByName_A = 5;
- logger.setLevel(Level.DEBUG); //FIXME #######################
+ //logger.setLevel(Level.DEBUG); //FIXME #######################
if (logger.isDebugEnabled()) {
for (int i = 0; i < results.size(); i++) {
String nameCache = "";
- TaxonNameBase<?,?> taxonNameBase= results.get(i).getName();
- nameCache = HibernateProxyHelper.deproxy(taxonNameBase, NonViralName.class).getNameCache();
+ TaxonName taxonName= results.get(i).getName();
+ nameCache = taxonName.getNameCache();
logger.debug(results.get(i).getClass() + "(" + i +")" +
": Name Cache = " + nameCache + ", Title Cache = " + results.get(i).getTitleCache());
}
assertEquals(numberOfTaxaByName_A, results.size());
+ includeUnpublished = false;
+ results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, accepted, includeUnpublished, null, null);
+ assertEquals(numberOfTaxaByName_A, results.size()); // no unpublished yet
+
//System.err.println("Species group: " + Rank.SPECIESGROUP().getId() + "Species: " + Rank.SPECIES().getId() + "Section Botany: "+ Rank.SECTION_BOTANY());
// assertEquals(results.get(4).getTitleCache(), "Abies alba Michx. sec. ???");
// assertEquals(results.get(5).getTitleCache(), "Abies alba Mill. sec. ???");
- results = taxonDao.getTaxaByName("A", MatchMode.BEGINNING, true, null, null);
+ includeUnpublished = true;
+ results = taxonDao.getTaxaByName("A*", MatchMode.BEGINNING, accepted, includeUnpublished, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertEquals(numberOfTaxaByName_A, results.size());
- results = taxonDao.getTaxaByName("Aus", MatchMode.EXACT, true, null, null);
+ results = taxonDao.getTaxaByName("Aus", MatchMode.EXACT, accepted, includeUnpublished, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertEquals("Results list should contain one entity",1,results.size());
}
public void testGetTaxaByNameWithMisappliedNames(){
Classification classification = classificationDao.load(classificationUuid);
-
+ TaxonNode subtree = null;
/* NOTE:
- * The testdata contains 3 misapplied names (1. nameCache = Aus, 2. nameCache = Rethera, 3. nameCache = Daphnis), two contained in the classification used in this test,
- * the other one is not contained in any classification. This latter case is the more general situation.
+ * The testdata contains 3 misapplied names (1. nameCache = Aus, 2. nameCache = Rethera, 3. nameCache = Daphnis),
+ * two contained in the classification used in this test,
+ * the other one is not contained in any classification. This later case is the more general situation.
* Misapplied names should be found regardless of whether they are contained in a classification or not.
*/
//two accepted taxa starting with R in classification "TestBaum"
- List<TaxonBase> results = taxonDao.getTaxaByName(true, false, false, "R*", classification, MatchMode.BEGINNING, null, null, null, null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "R*", classification, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 2 Taxa", 2, results.size());
//three taxa, 2 accepted and 1 misapplied name starting with R
- results = taxonDao.getTaxaByName(true, false, true, "R*", null, MatchMode.BEGINNING, null, null, null, null);
+ results = taxonDao.getTaxaByName(doTaxa, noSynonyms, doMisapplied, noCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 3 Taxa", 3, results.size());
- //one synonym is not in a synonymrelationship
- results = taxonDao.getTaxaByName(true, true, true, "A*", null, MatchMode.BEGINNING, null, null, null, null);
+ //one synonym has no accepted taxon
+ results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "A*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 11 Taxa",11, results.size());
//two accepted taxa in classification and 1 misapplied name with accepted name in classification
- results = taxonDao.getTaxaByName(true, true, true, "R*", classification, MatchMode.BEGINNING, null, null, null, null);
+ results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", classification, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 3 Taxa", 3, results.size());
+ //same with unpublished
+ includeUnpublished = false;
+ results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", classification, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 3 Taxa", 3, results.size());
+ includeUnpublished = true;
+
//same as above because all taxa, synonyms and misapplied names starting with R are in the classification
- results = taxonDao.getTaxaByName(true, true, true, "R*", null, MatchMode.BEGINNING, null, null, null, null);
+ results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 3 Taxa", 3, results.size());
//find misapplied names with accepted taxon in the classification, the accepted taxa of two misapplied names are in the classification
- results = taxonDao.getTaxaByName(false, false, true, "*", classification, MatchMode.BEGINNING, null, null, null, null);
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "*", classification, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 2 Taxa", 2, results.size());
//find misapplied names beginning with R
- results = taxonDao.getTaxaByName(false, false, true, "R*", null, MatchMode.BEGINNING, null, null, null, null);
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 1 Taxa", 1, results.size());
//find all three misapplied names
- results = taxonDao.getTaxaByName(false, false, true, "*", null, MatchMode.BEGINNING, null, null, null, null);
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Assert.assertEquals("There should be 3 Taxa", 3, results.size());
}
+ /**
+ * Test for all not covered possibilities of searches
+ */
+ @Test
+ @DataSet (loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
+ public void testGetTaxaByNameVariants(){
+ TaxonNode subtree = null;
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 2 Taxa",2, results.size());
+
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, doCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 1 Taxa", 1, results.size());
+
+ results = taxonDao.getTaxaByName(noTaxa, doSynonyms, doMisapplied, doCommonNames, false, "R*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 1 Taxa", 1, results.size());
+
+ results = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 2 Taxa", 2, results.size());
+
+ results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 2 Taxa", 2, results.size());
+
+ Classification classification = classificationDao.load(classificationUuid);
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", classification, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 1 Taxa", 1, results.size());
+
+ Set<NamedArea> namedAreas = new HashSet<>();
+ namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, subtree, MatchMode.BEGINNING,
+ namedAreas, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("There should be 1 Taxa", 1, results.size());
+ }
/**
* Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
@Test
@DataSet
public void testGetTaxaByNameForEditor() {
- Reference<?> sec = referenceDao.findById(1);
+ TaxonNode subtree = null;
+ Reference sec = referenceDao.findById(1);
assert sec != null : "sec must exist";
- List<UuidAndTitleCache<IdentifiableEntity>> results = taxonDao.getTaxaByNameForEditor(true, true, false,false,"Mand*", null, MatchMode.BEGINNING, null);
+ @SuppressWarnings("rawtypes")
+ List<UuidAndTitleCache<? extends IdentifiableEntity>> results = taxonDao.getTaxaByNameForEditor(
+ doTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "Acher", null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
- //assertFalse("The list should not be empty", results.isEmpty());
- assertTrue(results.size() == 5);
+ assertFalse("The list should not be empty", results.isEmpty());
+ assertEquals(4, results.size());
- results = taxonDao.getTaxaByNameForEditor(true, true, false, false,"A*",null, MatchMode.BEGINNING, null);
+ results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,includeUnpublished, "A",null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
- assertEquals(results.size(), 12);
+ assertEquals(7, results.size());
- results = taxonDao.getTaxaByNameForEditor(true, false,false, false,"A", null,MatchMode.BEGINNING, null);
+ results = taxonDao.getTaxaByNameForEditor(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
- assertTrue(results.size() == 9);
+ assertEquals(5, results.size());
assertEquals(results.get(0).getType(), Taxon.class);
- results = taxonDao.getTaxaByNameForEditor(false, true,false,false, "A", null,MatchMode.BEGINNING, null);
+ results = taxonDao.getTaxaByNameForEditor(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
- assertTrue(results.size() == 3);
+ assertEquals(2, results.size());
assertEquals(results.get(0).getType(), Synonym.class);
- results = taxonDao.getTaxaByNameForEditor(true, true,false,false,"Aus", null,MatchMode.EXACT, null);
+ results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,includeUnpublished, "Aus", null, subtree, MatchMode.EXACT, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertEquals("Results list should contain one entity",1,results.size());
- results = taxonDao.getTaxaByNameForEditor(true, true,true,false,"A*", null,MatchMode.BEGINNING, null);
+ results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
- assertEquals("Results list should contain one entity",15,results.size());
+ assertEquals("Results list should contain one entity", 8, results.size());
//TODO: test the search for misapplied names
@Test
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
public void testGetTaxaByNameAndArea() {
-
- Set<NamedArea> namedAreas = new HashSet<NamedArea>();
+ TaxonNode subtree = null;
+ Set<NamedArea> namedAreas = new HashSet<>();
namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
//namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
//namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
- Classification taxonmicTree = classificationDao.findByUuid(classificationUuid);
+ Classification classification = classificationDao.findByUuid(classificationUuid);
// prepare some synonym relation ships for some tests
Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
- taxonRethera.addSynonym(synAtroposAgassiz, SynonymRelationshipType.SYNONYM_OF());
- logger.warn("addSynonym(..)");
- //this.taxonDao.clear();
+ taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
+// logger.warn("addSynonym(..)");
+
Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
- Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
- taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymRelationshipType.SYNONYM_OF());
- this.taxonDao.save(taxonRetheraSecCdmtest);
- //this.taxonDao.clear();
+ Taxon taxonRetheraSecCdmTest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
+ taxonRetheraSecCdmTest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
+ this.taxonDao.save(taxonRetheraSecCdmTest);
+
Taxon test = (Taxon)this.taxonDao.findByUuid(retheraSecCdmtest);
- Set<Synonym> synonyms = test.getSynonyms();
+// Set<Synonym> synonyms3 = test.getSynonyms();
// 1. searching for a taxon (Rethera)
//long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
- List<TaxonBase> results = taxonDao.getTaxaByName(true,false, false, "Rethera", null, MatchMode.BEGINNING, namedAreas,
- null, null, null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", null, subtree, MatchMode.BEGINNING, namedAreas,
+ includeUnpublished, null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
+ results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "com*", null, subtree, MatchMode.BEGINNING, namedAreas,
+ includeUnpublished, null, null, null, null);
+ assertNotNull("getTaxaByName should return a List", results);
+ assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
+
// 2. searching for a taxon (Rethera) contained in a specific classification
- results = taxonDao.getTaxaByName(true, false, false, "Rethera", taxonmicTree, MatchMode.BEGINNING, namedAreas,
- null, null, null);
+ results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", classification, subtree, MatchMode.BEGINNING, namedAreas,
+ includeUnpublished, null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
// 3. searching for Synonyms
- results = taxonDao.getTaxaByName(false, true, false, "Atropo", null, MatchMode.ANYWHERE, null,
- null, null, null);
+ results = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Atropo", null, subtree, MatchMode.ANYWHERE, null,
+ includeUnpublished, null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
/*System.err.println(results.get(0).getTitleCache() + " - " +results.get(1).getTitleCache() + " - " +results.get(2).getTitleCache() );
assertTrue("expected to find three taxa but found "+results.size(), results.size() == 3);
// 4. searching for Synonyms
- results = taxonDao.getTaxaByName(false, true, false, "Atropo", null, MatchMode.BEGINNING, null,
- null, null, null);
+ results = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false,"Atropo", null, subtree, MatchMode.BEGINNING, null,
+ includeUnpublished, null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find three taxa but found "+results.size(), results.size() == 3);
// 5. searching for a Synonyms and Taxa
- // create a synonym relationship first
- results = taxonDao.getTaxaByName(true, true, false, "A", null, MatchMode.BEGINNING, namedAreas,
- null, null, null);
+ results = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"A", null, subtree, MatchMode.BEGINNING, namedAreas,
+ includeUnpublished, null, null, null, null);
//only five taxa have a distribution
assertNotNull("getTaxaByName should return a List", results);
- assertTrue("expected to find 7 taxa but found "+results.size(), results.size() == 8);
+ assertTrue("expected to find 8 taxa but found "+results.size(), results.size() == 8);
}
/**
- * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#findByNameTitleCache(Class<? extends TaxonBase>clazz, String queryString, Classification classification, MatchMode matchMode, Set<NamedArea> namedAreas, Integer pageNumber, Integer pageSize, List<String> propertyPaths)}
+ * 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)}
* restricting the search by a set of Areas.
*/
@Test
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
public void testFindByNameTitleCache() {
+ TaxonNode subtree = null;
- Set<NamedArea> namedAreas = new HashSet<NamedArea>();
+ Set<NamedArea> namedAreas = new HashSet<>();
namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
//namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
//namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
// prepare some synonym relation ships for some tests
Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
- taxonRethera.addSynonym(synAtroposAgassiz, SynonymRelationshipType.SYNONYM_OF());
- logger.warn("addSynonym(..)");
+ taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
+ //logger.warn("addSynonym(..)");
this.taxonDao.clear();
Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
- taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymRelationshipType.SYNONYM_OF());
+ taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
this.taxonDao.clear();
+
// 1. searching for a taxon (Rethera)
//long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
- List<TaxonBase> results = taxonDao.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", null, MatchMode.EXACT, namedAreas,
- null, null, null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> results = taxonDao.findByNameTitleCache(doTaxa, noSynonyms, includeUnpublished, "Rethera Rothschild & Jordan, 1903", null, subtree, MatchMode.EXACT, namedAreas,
+ null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
// 2. searching for a taxon (Rethera) contained in a specific classification
- results = taxonDao.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", classification, MatchMode.EXACT, namedAreas,
- null, null, null);
+ results = taxonDao.findByNameTitleCache(doTaxa, noSynonyms, includeUnpublished, "Rethera Rothschild & Jordan, 1903", classification, subtree, MatchMode.EXACT, namedAreas,
+ null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find one taxon but found "+results.size(), results.size() == 1);
-
// 3. searching for Synonyms
- results = taxonDao.findByNameTitleCache(false, true, "Atropo", null, MatchMode.ANYWHERE, null,
- null, null, null);
+ results = taxonDao.findByNameTitleCache(noTaxa, doSynonyms, includeUnpublished, "*Atropo", null, subtree, MatchMode.ANYWHERE, null,
+ null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
-
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
// 4. searching for Synonyms
- results = taxonDao.findByNameTitleCache(false, true, "Atropo", null, MatchMode.BEGINNING, null,
- null, null, null);
+ results = taxonDao.findByNameTitleCache(noTaxa, doSynonyms, includeUnpublished, "Atropo", null, subtree, MatchMode.BEGINNING, null,
+ null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find two taxa but found "+results.size(), results.size() == 2);
-
// 5. searching for a Synonyms and Taxa
- // create a synonym relationship first
+ // attache a synonym first
Synonym syn = (Synonym)taxonDao.findByUuid(this.atroposLeach);
Taxon tax = (Taxon) taxonDao.findByUuid(rethera);
- tax.addSynonym(syn, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
+ tax.addSynonym(syn, SynonymType.HETEROTYPIC_SYNONYM_OF());
taxonDao.save(tax);
- results = taxonDao.findByNameTitleCache(true, true, "A", null, MatchMode.BEGINNING, namedAreas,
- null, null, null);
+ results = taxonDao.findByNameTitleCache(doTaxa, doSynonyms, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, namedAreas,
+ null, null, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertTrue("expected to find 8 taxa but found "+results.size(), results.size() == 8);
}
@Test
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
public void testTaxonNameInTwoClassifications(){
- int numberOfClassifications = classificationDao.count();
- List<String> propertyPaths = new ArrayList<String>();
+ TaxonNode subtree = null;
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("taxonNodes");
- List<TaxonBase> taxa = taxonDao.getTaxaByName(true, true, false, "P*", null, MatchMode.BEGINNING, null, null, null, null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> taxa = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"P", null, subtree, MatchMode.BEGINNING,
+ null, includeUnpublished, null, null, null, null);
Taxon taxon = (Taxon)taxa.get(0);
Set<TaxonNode> nodes = taxon.getTaxonNodes();
assertTrue(nodes.size() == 1);
//assertTrue(taxa.size() > 0);
}
+ @Test
+ @DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
+ public void testGetTaxaByNameProParteSynonym(){
+ TaxonNode subtree = null;
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> taxa = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", null,subtree,
+ MatchMode.BEGINNING, null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("2 synonyms and 1 pro parte synonym should be returned.", 3, taxa.size());
+ assertTrue("Pro parte should exist", existsInCollection(taxa, acherontiaLachesis));
+ assertTrue("Normal synonym should exist", existsInCollection(taxa, atroposAgassiz));
+ assertTrue("2. normal synonym should exist", existsInCollection(taxa, atroposOken));
+ //TODO shouldn't we also find orphaned synonyms (without accepted taxon) like Atropos Leach?
+
+ taxa = taxonDao.getTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", null,subtree,
+ MatchMode.BEGINNING, null, NO_UNPUBLISHED, null, null, null, null);
+ Assert.assertEquals("2 synonyms and no pro parte synonym should be returned.", 2, taxa.size());
+ assertTrue("Normal synonym should exist", existsInCollection(taxa, atroposAgassiz));
+ assertTrue("2. normal synonym should exist", existsInCollection(taxa, atroposOken));
+
+ taxa = taxonDao.getTaxaByName(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "A", null,subtree,
+ MatchMode.BEGINNING, null, includeUnpublished, null, null, null, null);
+ Assert.assertEquals("1 misapplied name, no pro parte synonym should be returned.", 1, taxa.size());
+ assertTrue("Pro parte should exist", existsInCollection(taxa, aus));
+
+ }
+
@Test
@DataSet
public void testFindByUuid() {
Taxon taxon = (Taxon)taxonDao.findByUuid(uuid);
- assertNotNull("findByUuid should return a taxon",taxon);
+ assertNotNull("findByUuid should return a taxon", taxon);
assertFalse("findByUuid should not return a taxon with it's name initialized",Hibernate.isInitialized(taxon.getName()));
}
@Test
@DataSet
public void testLoad() {
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("name");
propertyPaths.add("sec");
Taxon taxon = (Taxon)taxonDao.load(uuid, propertyPaths);
@Test
@DataSet
- public void testCountTaxonRelationships() {
+ public void testCountTaxonRelationshipsByTaxon() {
Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon must exist";
- int numberOfRelatedTaxa = taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship.Direction.relatedTo);
- assertEquals("countTaxonRelationships should return 23", 23, numberOfRelatedTaxa);
+ long numberOfRelatedTaxa = taxonDao.countTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, TaxonRelationship.Direction.relatedTo);
+ assertEquals("countTaxonRelationships should return 8", 8, numberOfRelatedTaxa);
}
@Test
@DataSet
public void testCountTaxaByName() {
- long numberOfTaxa = taxonDao.countTaxaByName(true, false, false, "A*", null, MatchMode.BEGINNING, null);
- assertEquals(numberOfTaxa, 9);
- numberOfTaxa = taxonDao.countTaxaByName(true, false, false, "Aus aus", null, MatchMode.EXACT, null);
- assertEquals(numberOfTaxa, 1);
- numberOfTaxa = taxonDao.countTaxaByName(false, true, false, "A*", null, MatchMode.BEGINNING, null);
- assertEquals(numberOfTaxa, 3);
- numberOfTaxa = taxonDao.countTaxaByName(true, true, false, "A*", null, MatchMode.BEGINNING, null);
- assertEquals(numberOfTaxa,12);
- numberOfTaxa = taxonDao.countTaxaByName(true, true, false, "Aasfwerfwf fffe", null, MatchMode.BEGINNING, null);
- assertEquals(numberOfTaxa, 0);
-// FIXME implement test for search in specific classification
-// Reference reference = referenceDao.findByUuid(UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2"));
-// numberOfTaxa = taxonDao.countTaxaByName("A*", MatchMode.BEGINNING, SelectMode.ALL, null, null);
-// assertEquals(numberOfTaxa, 2);
+ TaxonNode subtree = null;
+ Classification classification= null;
+ long numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames,false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals(5, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "S", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("Sphingidae, Smerinthus, Smerinthus kindermannii and Sphingonaepiopsis expected", 4, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Smerinthus kindermannii", classification, subtree, MatchMode.EXACT, null, includeUnpublished);
+ assertEquals(1, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals(2, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals(7, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Aasfwerfwf fffe", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals(0, numberOfTaxa);
+
+ subtree = taxonNodeDao.findByUuid(UUID_ACHERONTIA_NODE);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("Acherontia and 2 A. species expected", 3, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "S", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("", 0, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Smerinthus kindermannii", classification, subtree, MatchMode.EXACT, null, includeUnpublished);
+ assertEquals("Smerinthus is not in subtree", 0, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("Atropos Agassiz and Atropos Oken expected as Synonyms", 2, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("The above accepted and synonyms expected", 5, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Aasfwerfwf fffe", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals(0, numberOfTaxa);
+
+ classification = classificationDao.findByUuid(UUID_CLASSIFICATION2);
+ subtree = null;
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("Acherontia and 2 A. species expected", 3, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "S", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("Sphingidae expected", 1, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Smerinthus kindermannii", classification, subtree, MatchMode.EXACT, null, includeUnpublished);
+ assertEquals("Smerinthus is not in subtree", 0, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("Atropos Agassiz and Atropos Oken expected as Synonyms", 2, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals("The above accepted and synonyms expected", 5, numberOfTaxa);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Aasfwerfwf fffe", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ assertEquals(0, numberOfTaxa);
}
@Test
Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon must exist";
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("fromTaxon");
propertyPaths.add("fromTaxon.name");
- List<OrderHint> orderHints = new ArrayList<OrderHint>();
+ List<OrderHint> orderHints = new ArrayList<>();
orderHints.add(new OrderHint("relatedFrom.name.genusOrUninomial", SortOrder.ASCENDING));
orderHints.add(new OrderHint("relatedFrom.name.specificEpithet", SortOrder.ASCENDING));
orderHints.add(new OrderHint("relatedFrom.name.infraSpecificEpithet", SortOrder.ASCENDING));
- List<TaxonRelationship> relatedTaxa = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), null, null, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
+ long count = taxonDao.countTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, TaxonRelationship.Direction.relatedTo);
+ assertEquals("Count should return 8 (related taxa)", 8, count);
+
+ List<TaxonRelationship> relatedTaxa = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, null, null, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
assertNotNull("getRelatedTaxa should return a List",relatedTaxa);
- assertEquals("getRelatedTaxa should return all 23 related taxa",relatedTaxa.size(),23);
+ assertEquals("getRelatedTaxa should return all 8 related taxa", 8, relatedTaxa.size());
assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate.isInitialized(relatedTaxa.get(0).getFromTaxon()));
assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate.isInitialized(relatedTaxa.get(0).getFromTaxon().getName()));
assertEquals("Acherontia should appear first in the list of related taxa", relatedTaxa.get(0).getFromTaxon().getTitleCache(), "Acherontia Laspeyres, 1809 sec. cate-sphingidae.org");
- assertEquals("Sphingonaepiopsis should appear last in the list of related taxa", relatedTaxa.get(22).getFromTaxon().getTitleCache(), "Sphinx Linnaeus, 1758 sec. cate-sphingidae.org");
+ 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());
}
@Test
Taxon taxon = (Taxon)taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon must exist";
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("fromTaxon");
propertyPaths.add("fromTaxon.name");
- List<OrderHint> orderHints = new ArrayList<OrderHint>();
+ List<OrderHint> orderHints = new ArrayList<>();
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
- List<TaxonRelationship> firstPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), 10, 0, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
- List<TaxonRelationship> secondPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),10, 1, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
- List<TaxonRelationship> thirdPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), 10, 2, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
-
- assertNotNull("getRelatedTaxa: 10, 0 should return a List",firstPage);
- assertEquals("getRelatedTaxa: 10, 0 should return a List with 10 elements",10,firstPage.size());
- assertNotNull("getRelatedTaxa: 10, 1 should return a List",secondPage);
- assertEquals("getRelatedTaxa: 10, 1 should return a List with 10 elements",secondPage.size(),10);
- assertNotNull("getRelatedTaxa: 10, 2 should return a List",thirdPage);
- assertEquals("getRelatedTaxa: 10, 2 should return a List with 3 elements",thirdPage.size(),3);
+ int pageSize = 3;
+ List<TaxonRelationship> firstPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, pageSize, 0, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
+ List<TaxonRelationship> secondPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, pageSize, 1, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
+ List<TaxonRelationship> thirdPage = taxonDao.getTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, pageSize, 2, orderHints,propertyPaths, TaxonRelationship.Direction.relatedTo);
+
+ assertNotNull("getRelatedTaxa: 3, 0 should return a List",firstPage);
+ assertEquals("getRelatedTaxa: 3, 0 should return a List with 3 elements", pageSize,firstPage.size());
+ assertNotNull("getRelatedTaxa: 3, 1 should return a List",secondPage);
+ assertEquals("getRelatedTaxa: 3, 1 should return a List with 3 elements", pageSize, secondPage.size());
+ assertNotNull("getRelatedTaxa: 3, 2 should return a List",thirdPage);
+ assertEquals("getRelatedTaxa: 3, 2 should return a List with 2 elements", 2, thirdPage.size());
}
@Test
@DataSet
- public void testCountSynonymRelationships() {
+ public void testCountSynonyms() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
assert taxon != null : "taxon must exist";
- int numberOfSynonymRelationships = taxonDao.countSynonyms(taxon,null);
- assertEquals("countSynonymRelationships should return 5",5,numberOfSynonymRelationships);
+ long numberOfRelatedSynonym = taxonDao.countSynonyms(taxon,null);
+ assertEquals("countSynonyms should return 3", 3, numberOfRelatedSynonym);
}
@Test
@DataSet
- public void testSynonymRelationships() {
+ public void testGetSynonyms() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
assert taxon != null : "taxon must exist";
List<String> propertyPaths = new ArrayList<String>();
propertyPaths.add("synonym");
propertyPaths.add("synonym.name");
- List<OrderHint> orderHints = new ArrayList<OrderHint>();
- orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
+ List<OrderHint> orderHints = new ArrayList<>();
+ orderHints.add(new OrderHint("titleCache", SortOrder.ASCENDING));
- List<SynonymRelationship> synonyms = taxonDao.getSynonyms(taxon, null, null, null,orderHints,propertyPaths);
+ List<Synonym> synonyms = taxonDao.getSynonyms(taxon, null, null, null,orderHints,propertyPaths);
- assertNotNull("getSynonyms should return a List",synonyms);
- assertEquals("getSynonyms should return 5 SynonymRelationship entities",synonyms.size(),5);
- assertTrue("getSynonyms should return SynonymRelationship objects with the synonym initialized",Hibernate.isInitialized(synonyms.get(0).getSynonym()));
+ assertNotNull("getSynonyms should return a List", synonyms);
+ assertEquals("getSynonyms should return 3 synonyms", 3, synonyms.size());
+ assertTrue("getSynonyms should return synonym objects with the synonym initialized", Hibernate.isInitialized(synonyms.get(0)));
}
@Test
@DataSet
- public void testCountSynonymRelationshipsByType() {
+ public void testCountSynonymsByType() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
assert taxon != null : "taxon must exist";
- int numberOfTaxonomicSynonyms = taxonDao.countSynonyms(taxon, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF());
- assertEquals("countSynonyms should return 4",numberOfTaxonomicSynonyms, 4);
+ long numberOfTaxonomicSynonyms = taxonDao.countSynonyms(taxon, SynonymType.HETEROTYPIC_SYNONYM_OF());
+ assertEquals("countSynonyms should return 4", 3, numberOfTaxonomicSynonyms);
}
@Test
@DataSet
- public void testSynonymRelationshipsByType() {
+ public void testSynonymsByType() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
assert taxon != null : "taxon must exist";
- List<SynonymRelationship> synonyms = taxonDao.getSynonyms(taxon, SynonymRelationshipType.HETEROTYPIC_SYNONYM_OF(), null, null,null,null);
+ List<Synonym> synonyms = taxonDao.getSynonyms(taxon, SynonymType.HETEROTYPIC_SYNONYM_OF(), null, null,null,null);
- assertNotNull("getSynonyms should return a List",synonyms);
- assertEquals("getSynonyms should return 4 SynonymRelationship entities",synonyms.size(),4);
+ assertNotNull("getSynonyms should return a List", synonyms);
+ assertEquals("getSynonyms should return 4 Synonyms", 3, synonyms.size());
}
@Test
@DataSet
- public void testPageSynonymRelationships(){
+ public void testPageSynonyms(){
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
assert taxon != null : "taxon must exist";
- List<SynonymRelationship> firstPage = taxonDao.getSynonyms(taxon, null, 4, 0,null,null);
- List<SynonymRelationship> secondPage = taxonDao.getSynonyms(taxon, null, 4, 1,null,null);
+ int pageSize = 2;
+ List<Synonym> firstPage = taxonDao.getSynonyms(taxon, null, pageSize, 0,null,null);
+ List<Synonym> secondPage = taxonDao.getSynonyms(taxon, null, pageSize, 1,null,null);
+
+ assertNotNull("getSynonyms: 2, 0 should return a List",firstPage);
+ assertEquals("getSynonyms: 2, 0 should return 2 synonyms", pageSize,firstPage.size());
+ assertNotNull("getSynonyms: 2, 1 should return a List",secondPage);
+ assertEquals("getSynonyms: 2, 1 should return 1 synonym", 1, secondPage.size());
+ }
+
+ @Test
+ @DataSet
+ public void testCountTaxonRelationships() {
+ long count = taxonDao.countTaxonRelationships(null);
+ assertEquals("There should be 11 relationships", 11, count);
+
+ Set<TaxonRelationshipType> types = new HashSet<>();
+ count = taxonDao.countTaxonRelationships(types);
+ assertEquals("Empty filter should return empty result", 0, count);
- assertNotNull("getSynonyms: 4, 0 should return a List",firstPage);
- assertEquals("getSynonyms: 4, 0 should return 4 SynonymRelationships", 4,firstPage.size());
- assertNotNull("getSynonyms: 4, 1 should return a List",secondPage);
- assertEquals("getSynonyms: 4, 1 should return 1 SynonymRelationship", 1, secondPage.size());
+ types.add(TaxonRelationshipType.CONGRUENT_TO());
+ count = taxonDao.countTaxonRelationships(types);
+ assertEquals("There should be no congruent relationship", 0, count);
+
+ types.add(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN());
+ count = taxonDao.countTaxonRelationships(types);
+ assertEquals("There should be 11 tax included relationships", 11, count);
+ }
+
+ @Test
+ @DataSet
+ public void testlistTaxonRelationships() {
+ List<TaxonRelationship> rels = taxonDao.getTaxonRelationships(null, null, null, null, null);
+ assertEquals("There should be 11 relationships", 11, rels.size());
+
+ rels = taxonDao.getTaxonRelationships(null, 2, 3, null, null);
+ assertEquals("There should be 11 relationships", 2, rels.size());
+
+ Set<TaxonRelationshipType> types = new HashSet<>();
+ rels = taxonDao.getTaxonRelationships(types, null, null, null, null);
+ assertEquals("Empty filter should return empty result", 0, rels.size());
+
+ types.add(TaxonRelationshipType.CONGRUENT_TO());
+ rels = taxonDao.getTaxonRelationships(types, null, null, null, null);
+ assertEquals("There should be no congruent relationship", 0, rels.size());
+
+ types.add(TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN());
+ rels = taxonDao.getTaxonRelationships(types, null, null, null, null);
+ assertEquals("There should be 11 tax included relationships", 11, rels.size());
}
@Test
Synonym synonym = (Synonym)taxonDao.findByUuid(acheontitia_ciprosus);
assertNotNull("synonym must exist", synonym);
- List<Taxon> list = taxonDao.listAcceptedTaxaFor(synonym, null, 4, 0, null, null);
- assertNotNull("listAcceptedTaxaFor should return a List");
- assertEquals("listAcceptedTaxaFor should return 2 Taxa", 2, list.size());
+ Taxon taxon = taxonDao.acceptedTaxonFor(synonym, null, null);
+ assertNotNull("listAcceptedTaxaFor should return a taxon", taxon);
Classification classification = classificationDao.load(classificationUuid);
assertNotNull("classification must exist", classification);
- list = taxonDao.listAcceptedTaxaFor(synonym, classification, 4, 0, null, null);
- assertNotNull("listAcceptedTaxaFor should return a List");
- assertEquals("listAcceptedTaxaFor should return 1 Taxa", 1, list.size());
+ taxon = taxonDao.acceptedTaxonFor(synonym, classification, null);
+ assertNull("listAcceptedTaxaFor should return not taxon due to classification filter", taxon);
}
@Test
@DataSet
public void testGetTaxonMatchingUninomial() {
- List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*",null,null,null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*","*",null,null,null);
assertNotNull("findTaxaByName should return a List", result);
assertEquals("findTaxaByName should return two Taxa",2,result.size());
@Test
@DataSet
public void testGetTaxonMatchingSpeciesBinomial() {
- List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Smerinthus", null, "kindermannii", null,null,null,null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", null, "kindermannii", null,"*",null,null,null);
assertNotNull("findTaxaByName should return a List", result);
assertEquals("findTaxaByName should return one Taxon",1,result.size());
@Test
@DataSet
public void testGetTaxonMatchingTrinomial() {
- List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis",null,null,null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis","*",null,null,null);
assertNotNull("findTaxaByName should return a List", result);
assertEquals("findTaxaByName should return one Taxon",1,result.size());
@Test
@DataSet
public void testNegativeMatch() {
- List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null);
+ @SuppressWarnings("rawtypes")
+ List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null,null);
assertNotNull("findTaxaByName should return a List", result);
assertTrue("findTaxaByName should return an empty List",result.isEmpty());
@Test
@DataSet
public void testCountAllTaxa() {
- int numberOfTaxa = taxonDao.count(Taxon.class);
- assertEquals("count should return 33 taxa",33, numberOfTaxa);
+ long numberOfTaxa = taxonDao.count(Taxon.class);
+ assertEquals("count should return 14 taxa", 14, numberOfTaxa);
}
@Test
@DataSet
public void testListAllTaxa() {
List<Taxon> taxa = taxonDao.list(Taxon.class,100, 0);
- assertNotNull("list should return a List",taxa);
- assertEquals("list should return 33 taxa",33, taxa.size());
+ assertNotNull("list should return a List", taxa);
+ assertEquals("list should return 14 taxa", 14, taxa.size());
}
@Test
assert taxon == null : "taxon must not exist";
setComplete();
endTransaction();
- try {
- printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
+// try {
+// printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
+// } catch (FileNotFoundException e) {
+// e.printStackTrace();
+// }
}
@Test
@DataSet
- // @ExpectedDataSet("TaxonDaoHibernateImplTest.testDelete-result.xml")
+ @ExpectedDataSet("TaxonDaoHibernateImplTest.testDelete-result.xml")
public void testDeleteWithMarker() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontia);
taxon.addMarker(Marker.NewInstance(MarkerType.IS_DOUBTFUL(), true));
assert taxon == null : "taxon must not exist";
setComplete();
endTransaction();
- try {
- printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
- } catch (FileNotFoundException e) {
- e.printStackTrace();
- }
- }
-
- @Test
- @DataSet
- public void testDeleteWithChildren() {
- Taxon taxonWithChildren = (Taxon)taxonDao.findByUuid(mimas);
- assert taxonWithChildren != null : "taxon must exist";
- assertEquals(taxonWithChildren.getTaxonomicChildrenCount(), 2);
- Taxon parent = (Taxon)taxonDao.findByUuid(sphingidae);
- assertSame(taxonWithChildren.getTaxonomicParent(), parent);
- assertEquals(parent.getTaxonomicChildrenCount(), 204);
- taxonDao.delete(taxonWithChildren);
- assertEquals(parent.getTaxonomicChildrenCount(), 203);
+// try {
+// printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
+// } catch (FileNotFoundException e) {
+// e.printStackTrace();
+// }
}
@Test
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon cannot be null";
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("name");
propertyPaths.add("createdBy");
propertyPaths.add("updatedBy");
+ @SuppressWarnings("rawtypes")
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(taxon, null,null,null,propertyPaths);
assertNotNull("getAuditEvents should return a list",auditEvents);
assertFalse("the list should not be empty",auditEvents.isEmpty());
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon cannot be null";
+ @SuppressWarnings("rawtypes")
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(taxon, null,null,AuditEventSort.FORWARDS,null);
assertNotNull("getAuditEvents should return a list",auditEvents);
assertFalse("the list should not be empty",auditEvents.isEmpty());
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon cannot be null";
- int numberOfAuditEvents = taxonDao.countAuditEvents(taxon,null);
+ long numberOfAuditEvents = taxonDao.countAuditEvents(taxon, null);
assertEquals("countAuditEvents should return 2",numberOfAuditEvents,2);
}
@DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
public void getPreviousAuditEventAtBeginning() {
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
- TaxonBase taxon = taxonDao.findByUuid(sphingidae);
+ TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon cannot be null";
+ @SuppressWarnings("rawtypes")
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getPreviousAuditEvent(taxon);
assertNull("getPreviousAuditEvent should return null if we're at the first audit event anyway",auditEvent);
}
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon cannot be null";
+ @SuppressWarnings("rawtypes")
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getNextAuditEvent(taxon);
assertNotNull("getNextAuditEvent should not return null as there is at least one audit event after the current one",auditEvent);
}
TaxonBase<?> taxon = taxonDao.findByUuid(sphingidae);
assert taxon != null : "taxon cannot be null";
+ @SuppressWarnings("rawtypes")
AuditEventRecord<TaxonBase> auditEvent = taxonDao.getNextAuditEvent(taxon);
assertNull("getNextAuditEvent should return null as there no more audit events after the current one",auditEvent);
}
- @Test
- @DataSet
- @ExpectedDataSet
- public void testAddChild() throws Exception {
- Taxon parent = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
- assert parent != null : "taxon cannot be null";
- Taxon child = Taxon.NewInstance(null, null);
- child.setTitleCache("Acherontia lachesis diehli Eitschberger, 2003", true);
- child.addTaxonRelation(parent, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),null, null);
- taxonDao.save(child);
- setComplete();
- endTransaction();
- }
-
@Test
@DataSet("TaxonDaoHibernateImplTest.testFind.xml")
public void testFind() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
assert taxon != null : "taxon cannot be null";
- assertEquals("getTaxonomicChildrenCount should return 1 in this view",1,taxon.getTaxonomicChildrenCount());
- assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon.getRelationsToThisTaxon().size());
+ assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon.getRelationsToThisTaxon().size());
}
@Test
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
assert taxon != null : "taxon cannot be null";
- assertEquals("getTaxonomicChildrenCount should return 0 in this view",0,taxon.getTaxonomicChildrenCount());
assertTrue("getRelationsToThisTaxon should contain 0 TaxonRelationship in this view",taxon.getRelationsToThisTaxon().isEmpty());
}
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
assert taxon != null : "taxon cannot be null";
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("fromTaxon");
propertyPaths.add("fromTaxon.name");
- List<OrderHint> orderHints = new ArrayList<OrderHint>();
+ List<OrderHint> orderHints = new ArrayList<>();
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
- List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
+ List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
assertNotNull("getRelatedTaxa should return a list", taxonRelations);
assertEquals("there should be one TaxonRelationship in the list in the current view",1,taxonRelations.size());
assertTrue("TaxonRelationship.relatedFrom should be initialized",Hibernate.isInitialized(taxonRelations.get(0).getFromTaxon()));
public void testCountRelations() {
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
assert taxon != null : "taxon cannot be null";
- assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship.Direction.relatedTo));
+ assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao.countTaxonRelationships(
+ taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, TaxonRelationship.Direction.relatedTo));
}
@Test
propertyPaths.add("relatedFrom");
propertyPaths.add("relatedFrom.name");
- List<OrderHint> orderHints = new ArrayList<OrderHint>();
+ List<OrderHint> orderHints = new ArrayList<>();
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
- List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
+ List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, null, null, orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
assertNotNull("getRelatedTaxa should return a list",taxonRelations);
- assertTrue("there should be no TaxonRelationships in the list in the prior view",taxonRelations.isEmpty());
+ assertTrue("there should be no TaxonRelationships in the list in the prior view", taxonRelations.isEmpty());
}
@Test
AuditEventContextHolder.getContext().setAuditEvent(previousAuditEvent);
Taxon taxon = (Taxon)taxonDao.findByUuid(acherontiaLachesis);
assert taxon != null : "taxon cannot be null";
- assertEquals("countRelatedTaxa should return 0 in the current view",0, taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship.Direction.relatedTo));
+ assertEquals("countRelatedTaxa should return 0 in the current view",0,
+ taxonDao.countTaxonRelationships(taxon,TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
+ includeUnpublished, TaxonRelationship.Direction.relatedTo));
}
@Test
@DataSet
public void testGroupTaxa() {
- List<Grouping> groups = new ArrayList<Grouping>();
+ List<Grouping> groups = new ArrayList<>();
groups.add(new GroupByCount("count",SortOrder.DESCENDING));
groups.add(new Grouping("name.genusOrUninomial", "genus", "n", SortOrder.ASCENDING));
List<Object[]> results = taxonDao.group(null, null, null, groups,null);
- System.out.println("count\tname.genuOrUninomial");
- for(Object[] result : results) {
- System.out.println(result[0] + "\t" + result[1]);
+ if(logger.isTraceEnabled()){
+ System.out.println("count\tname.genuOrUninomial");
+ for(Object[] result : results) {
+ System.out.println(result[0] + "\t" + result[1]);
+ }
}
}
@Test
@DataSet
public void testGroupTaxaByClass() {
- List<Grouping> groups = new ArrayList<Grouping>();
+ List<Grouping> groups = new ArrayList<>();
groups.add(new GroupByCount("count",SortOrder.DESCENDING));
groups.add(new Grouping("class", "class",null, SortOrder.ASCENDING));
List<Object[]> results = taxonDao.group(null, null, null, groups,null);
- System.out.println("count\tclass");
- for(Object[] result : results) {
- System.out.println(result[0] + "\t" + result[1]);
+ if(logger.isTraceEnabled()){
+ System.out.println("count\tclass");
+ for(Object[] result : results) {
+ System.out.println(result[0] + "\t" + result[1]);
+ }
}
}
@Test
@DataSet
public void testNativeSQLOrder() {
- List<OrderHint> orderHints = new ArrayList<OrderHint>();
+ List<OrderHint> orderHints = new ArrayList<>();
orderHints.add(new NativeSqlOrderHint("case when {alias}.titleCache like 'C%' then 0 else 1 end",SortOrder.ASCENDING));
+ @SuppressWarnings("rawtypes")
List<TaxonBase> results = taxonDao.list(null, null, orderHints);
- System.out.println("native SQL order");
- for(TaxonBase<?> result : results) {
- System.out.println(result.getTitleCache());
+ if(logger.isTraceEnabled()){
+ System.out.println("native SQL order");
+ for(TaxonBase<?> result : results) {
+ System.out.println(result.getTitleCache());
+ }
}
}
@Test
@DataSet
public void testGroupByDateTaxa() {
- List<Grouping> groups = new ArrayList<Grouping>();
+ List<Grouping> groups = new ArrayList<>();
groups.add(new GroupByCount("count",null));
groups.add(new GroupByDate("created", "dateGroup", SortOrder.ASCENDING, GroupByDate.Resolution.MONTH));
List<Object[]> results = taxonDao.group(null, null, null, groups,null);
- System.out.println("count\tyear\tmonth");
- for(Object[] result : results) {
- System.out.println(result[0] + "\t" + result[1] + "\t" + result[2]);
+ if(logger.isTraceEnabled()){
+ System.out.println("count\tyear\tmonth");
+ for(Object[] result : results) {
+ System.out.println(result[0] + "\t" + result[1] + "\t" + result[2]);
+ }
}
}
- @Test
- @DataSet ("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
- public final void testGetTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(){
- Classification classification = classificationDao.findByUuid(classificationUuid);
- List<UuidAndTitleCache<TaxonNode>> result = taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification);
- assertNotNull(result);
- assertEquals(5, result.size());
- UUID excludeUUID = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
- List<UUID> excludeUUids = new ArrayList<UUID>();
- excludeUUids.add(excludeUUID);
- result = taxonDao.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification, excludeUUids);
- assertEquals(4, result.size());
- }
@Test
public void testGetAuditEventsByTypeWithRestrictions() {
commitAndStartNewTransaction(new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("name");
propertyPaths.add("createdBy");
propertyPaths.add("updatedBy");
- List<AuditCriterion> criteria = new ArrayList<AuditCriterion>();
+ List<AuditCriterion> criteria = new ArrayList<>();
criteria.add(AuditEntity.property("lsid_lsid").isNotNull());
- int count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
+ long count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
+ @SuppressWarnings("rawtypes")
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(TaxonBase.class, previousAuditEvent, mostRecentAuditEvent, criteria,null, null, AuditEventSort.FORWARDS, propertyPaths);
assertNotNull("getAuditEvents should return a list",auditEvents);
assertFalse("the list should not be empty",auditEvents.isEmpty());
//while those inserted by the terms dataset are inserted as well as a completely new one.
//This problem for some reason does not happen if not running at first place
public void testGetAuditEventsByTypeWithNoRestrictions() {
- printDataSet(System.out, new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
+// printDataSet(System.out, new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
commitAndStartNewTransaction(new String[]{"AUDITEVENT", "TAXONBASE_AUD"});
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("name");
propertyPaths.add("createdBy");
propertyPaths.add("updatedBy");
- int count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
+ long count = taxonDao.countAuditEvents(TaxonBase.class, null, null, null);
+ @SuppressWarnings("rawtypes")
List<AuditEventRecord<TaxonBase>> auditEvents = taxonDao.getAuditEvents(TaxonBase.class, previousAuditEvent, mostRecentAuditEvent, null,null, null, AuditEventSort.FORWARDS, propertyPaths);
assertNotNull("getAuditEvents should return a list", auditEvents);
assertFalse("the list should not be empty", auditEvents.isEmpty());
- assertEquals("There should be thirty eight AuditEventRecords in the list", 38, auditEvents.size());
+ assertEquals("There should be thirty eight AuditEventRecords in the list", 2, auditEvents.size());
}
assertNotNull("getTaxaByCommonName should return a list", commonNameResults);
assertFalse("the list should not be empty", commonNameResults.isEmpty());
- assertEquals("There should be one Taxon with common name", 1,commonNameResults.size());
- assertEquals(" sec. ???", ((TaxonBase)commonNameResults.get(0)).getTitleCache());
+ assertEquals("There should be two taxa with common name", 2,commonNameResults.size());
+
+ List<UuidAndTitleCache<Taxon>> list = taxonDao.getTaxaByCommonNameForEditor(
+ "common%", null, MatchMode.BEGINNING, null);
+
+ assertNotNull("getTaxaByCommonName should return a list", list);
+ assertFalse("the list should not be empty", list.isEmpty());
+ assertEquals("There should be two Taxon with common name", 2,list.size());
+
}
+ @Test
+ @DataSet
+ public void testGetTitleCache(){
+ UUID uuid = UUID.fromString("7b8b5cb3-37ba-4dba-91ac-4c6ffd6ac331");
+ String titleCache = taxonDao.getTitleCache(uuid, false);
+ Assert.assertEquals("Acherontia styx Westwood, 1847 sec. cate-sphingidae.org", titleCache);
+ titleCache = taxonDao.getTitleCache(uuid, true);
+ Assert.assertEquals("Acherontia styxx Westwood, 1847 sec. cate-sphingidae.org", titleCache);
+ }
+
+
@Test
@DataSet("TaxonDaoHibernateImplTest.testPropertyPath.xml")
public void testPropertyPath(){
Taxon taxonProxy = singleNode.getTaxon();
Assert.assertTrue("Object to test should be a proxy ", taxonProxy instanceof HibernateProxy);
- List<String> propertyPaths = new ArrayList<String>();
+ List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("taxonNodes");
Taxon taxon = (Taxon)this.taxonDao.load(
UUID.fromString("4a5bc930-844f-45ec-aea8-dd155e1ab25f"),
Assert.assertSame("Returned object should be the same proxy to assure that we ran initialization on this proxy", taxonProxy, taxon);
}
+
/**
* {@inheritDoc}
*/
// @Test
public void createTestDataSet() throws FileNotFoundException {
// Classification classification = Classification.NewInstance("Test");
-// BotanicalName taxonNameBase = null;
-// Reference<?> sec = null;
-// Taxon taxon = Taxon.NewInstance(taxonNameBase, sec);
+// BotanicalName TaxonName = null;
+// Reference sec = null;
+// Taxon taxon = Taxon.NewInstance(taxonName, sec);
// classification.addChildTaxon(taxon, sec, null);
//
// classificationDao.save(classification);
// this.commitAndStartNewTransaction(null);
//
// writeDbUnitDataSetFile(new String[] {
-// "CLASSIFICATION", "TAXONNAMEBASE",
+// "CLASSIFICATION", "TAXONNAME",
// "REFERENCE","TAXONNODE",
// "TAXONBASE","LANGUAGESTRING",
// "HIBERNATE_SEQUENCES" // IMPORTANT!!!
BGBM BDI Projects / cdmlib.git / blobdiff