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.query.GroupByCount;
import eu.etaxonomy.cdm.persistence.query.GroupByDate;
@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 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;
+ @SuppressWarnings("unused")
private static final String[] TABLE_NAMES = new String[] {
"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");
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;
assertNotNull("Instance of IReferenceDao expected",referenceDao);
}
- /**
- * 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);
assert sec != null : "sec must exist";
+ @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());
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,
* 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(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "R*", classification, MatchMode.BEGINNING,
+ @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(doTaxa, noSynonyms, doMisapplied, noCommonNames, false, "R*", null, MatchMode.BEGINNING,
+ 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 has no accepted taxon
- results = taxonDao.getTaxaByName(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "A*", null, MatchMode.BEGINNING,
+ 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(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", classification, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, "R*", null, MatchMode.BEGINNING,
+ 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(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "*", classification, MatchMode.BEGINNING,
+ 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(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "R*", null, MatchMode.BEGINNING,
+ 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(noTaxa, noSynonyms, doMisapplied, noCommonNames, false, "*", null, MatchMode.BEGINNING,
+ 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
@DataSet (loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
public void testGetTaxaByNameVariants(){
- List<TaxonBase> results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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, MatchMode.BEGINNING,
+ 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
@DataSet
public void testGetTaxaByNameForEditor() {
+ TaxonNode subtree = null;
Reference sec = referenceDao.findById(1);
assert sec != null : "sec must exist";
@SuppressWarnings("rawtypes")
List<UuidAndTitleCache<? extends IdentifiableEntity>> results = taxonDao.getTaxaByNameForEditor(
- doTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "Acher", null, MatchMode.BEGINNING, null, null);
+ 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());
assertEquals(4, results.size());
- results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,includeUnpublished, "A",null, MatchMode.BEGINNING, null, 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(7, results.size());
- results = taxonDao.getTaxaByNameForEditor(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, MatchMode.BEGINNING, null, null);
+ results = taxonDao.getTaxaByNameForEditor(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertEquals(5, results.size());
assertEquals(results.get(0).getType(), Taxon.class);
- results = taxonDao.getTaxaByNameForEditor(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, MatchMode.BEGINNING, null, null);
+ results = taxonDao.getTaxaByNameForEditor(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, includeUnpublished, "A", null, subtree, MatchMode.BEGINNING, null, null);
assertNotNull("getTaxaByName should return a List", results);
assertEquals(2, results.size());
assertEquals(results.get(0).getType(), Synonym.class);
- results = taxonDao.getTaxaByNameForEditor(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,includeUnpublished, "Aus", null, MatchMode.EXACT, null, 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(doTaxa, doSynonyms, doMisapplied, noCommonNames, false, includeUnpublished, "A", null, MatchMode.BEGINNING, null, 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", 8, results.size());
@Test
@DataSet(loadStrategy=CleanSweepInsertLoadStrategy.class, value="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
public void testGetTaxaByNameAndArea() {
-
+ 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, SynonymType.SYNONYM_OF());
- logger.warn("addSynonym(..)");
+// logger.warn("addSynonym(..)");
Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
- Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
- taxonRetheraSecCdmtest.addSynonym(synAtroposLeach, SynonymType.SYNONYM_OF());
- this.taxonDao.save(taxonRetheraSecCdmtest);
+ 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> 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(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", null, MatchMode.BEGINNING, namedAreas,
+ @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, MatchMode.BEGINNING, namedAreas,
+ 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(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", taxonmicTree, MatchMode.BEGINNING, namedAreas,
+ 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(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "Atropo", null, MatchMode.ANYWHERE, 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(noTaxa, doSynonyms, noMisapplied, noCommonNames, false,"Atropo", null, MatchMode.BEGINNING, 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
- results = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"A", null, MatchMode.BEGINNING, namedAreas,
+ 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);
/**
- * 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<>();
namedAreas.add((NamedArea)definedTermDao.load(northernAmericaUuid));
Synonym synAtroposAgassiz = (Synonym)taxonDao.findByUuid(atroposAgassiz);
Taxon taxonRethera = (Taxon)taxonDao.findByUuid(rethera);
taxonRethera.addSynonym(synAtroposAgassiz, SynonymType.SYNONYM_OF());
- logger.warn("addSynonym(..)");
+ //logger.warn("addSynonym(..)");
this.taxonDao.clear();
Synonym synAtroposLeach = (Synonym)taxonDao.findByUuid(atroposLeach);
Taxon taxonRetheraSecCdmtest = (Taxon)taxonDao.findByUuid(retheraSecCdmtest);
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, includeUnpublished, "Rethera Rothschild & Jordan, 1903", null, MatchMode.EXACT, namedAreas,
+ @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, includeUnpublished, "Rethera Rothschild & Jordan, 1903", classification, MatchMode.EXACT, namedAreas,
+ 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, includeUnpublished, "*Atropo", null, MatchMode.ANYWHERE, 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, includeUnpublished, "Atropo", null, MatchMode.BEGINNING, 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
// attache a synonym first
Synonym syn = (Synonym)taxonDao.findByUuid(this.atroposLeach);
tax.addSynonym(syn, SynonymType.HETEROTYPIC_SYNONYM_OF());
taxonDao.save(tax);
- results = taxonDao.findByNameTitleCache(true, true, includeUnpublished, "A", null, MatchMode.BEGINNING, namedAreas,
+ 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(){
+ TaxonNode subtree = null;
List<String> propertyPaths = new ArrayList<>();
propertyPaths.add("taxonNodes");
- List<TaxonBase> taxa = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"P", null, MatchMode.BEGINNING,
+ @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(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() {
@Test
@DataSet
public void testCountTaxaByName() {
- long numberOfTaxa = taxonDao.countTaxaByName(true, false, false, false,false, "A", null, MatchMode.BEGINNING, null, includeUnpublished);
+ 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(true, false, false, false, false,"Smerinthus kindermannii", null, MatchMode.EXACT, null, includeUnpublished);
+ 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(false, true, false, false, false,"A", null, MatchMode.BEGINNING, null, includeUnpublished);
+ numberOfTaxa = taxonDao.countTaxaByName(noTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
assertEquals(2, numberOfTaxa);
- numberOfTaxa = taxonDao.countTaxaByName(true, true, false, false, false,"A", null, MatchMode.BEGINNING, null, includeUnpublished);
+ numberOfTaxa = taxonDao.countTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false, "A", classification, subtree, MatchMode.BEGINNING, null, includeUnpublished);
assertEquals(7, numberOfTaxa);
- numberOfTaxa = taxonDao.countTaxaByName(true, true, false, false,false, "Aasfwerfwf fffe", null, MatchMode.BEGINNING, null, includeUnpublished);
+ 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);
-// 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);
}
@Test
@Test
@DataSet
public void testGetTaxonMatchingUninomial() {
+ @SuppressWarnings("rawtypes")
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", "*", "*", "*","*",null,null,null);
assertNotNull("findTaxaByName should return a List", result);
@Test
@DataSet
public void testGetTaxonMatchingSpeciesBinomial() {
+ @SuppressWarnings("rawtypes")
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class, "Smerinthus", null, "kindermannii", null,"*",null,null,null);
assertNotNull("findTaxaByName should return a List", result);
@Test
@DataSet
public void testGetTaxonMatchingTrinomial() {
+ @SuppressWarnings("rawtypes")
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Cryptocoryne", null,"purpurea","borneoensis","*",null,null,null);
assertNotNull("findTaxaByName should return a List", result);
@Test
@DataSet
public void testNegativeMatch() {
+ @SuppressWarnings("rawtypes")
List<TaxonBase> result = taxonDao.findTaxaByName(Taxon.class,"Acherontia", null,"atropos","dehli",null,null,null,null);
assertNotNull("findTaxaByName should return a List", result);
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());
@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);
}
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(),
+ assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao.countTaxonRelationships(
+ taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
includeUnpublished, TaxonRelationship.Direction.relatedTo));
}
orderHints.add(new OrderHint("relatedFrom.titleCache", SortOrder.ASCENDING));
List<TaxonRelationship> taxonRelations = taxonDao.getTaxonRelationships(taxon, TaxonRelationshipType.TAXONOMICALLY_INCLUDED_IN(),
- includeUnpublished, null, null,orderHints,propertyPaths, TaxonRelationship.Direction.relatedFrom);
+ 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
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);
if(logger.isTraceEnabled()){
System.out.println("native SQL order");
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<>();
propertyPaths.add("createdBy");
propertyPaths.add("updatedBy");
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());
assertFalse("the list should not be empty", commonNameResults.isEmpty());
assertEquals("There should be two taxa with common name", 2,commonNameResults.size());
- List<UuidAndTitleCache<IdentifiableEntity>> list = taxonDao.getTaxaByCommonNameForEditor(
+ List<UuidAndTitleCache<Taxon>> list = taxonDao.getTaxaByCommonNameForEditor(
"common%", null, MatchMode.BEGINNING, null);
assertNotNull("getTaxaByCommonName should return a list", list);
BGBM BDI Projects / cdmlib.git / blobdiff