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;
@SpringBeanByType
private IDefinedTermDao definedTermDao;
- private UUID uuid;
- private UUID sphingidae;
- private UUID acherontia;
- private UUID rethera;
- private UUID retheraSecCdmtest;
- private UUID atroposAgassiz; // a Synonym
- private UUID atroposOken; // a Synonym
- private UUID atroposLeach; // a Synonym
- private UUID acherontiaLachesis;
- private UUID aus;
+ 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;
@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");
- atroposOken = UUID.fromString("6bfedf25-6dbc-4d5c-9d56-84f9052f3b2a");
- atroposLeach = UUID.fromString("3da4ab34-6c50-4586-801e-732615899b07");
- rethera = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
- retheraSecCdmtest = UUID.fromString("a9f42927-e507-4fda-9629-62073a908aae");
- aus = UUID.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
previousAuditEvent = new AuditEvent();
previousAuditEvent.setRevisionNumber(1025);
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,
*/
//two accepted taxa starting with R in classification "TestBaum"
@SuppressWarnings("rawtypes")
- List<TaxonBase> results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "R*", classification, MatchMode.BEGINNING,
+ 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(){
+ TaxonNode subtree = null;
@SuppressWarnings("rawtypes")
- List<TaxonBase> results = taxonDao.getTaxaByName(noTaxa, noSynonyms, noMisapplied, doCommonNames, false, "c*", null, MatchMode.BEGINNING,
+ 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);
//long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
@SuppressWarnings("rawtypes")
- List<TaxonBase> results = taxonDao.getTaxaByName(doTaxa, noSynonyms, noMisapplied, noCommonNames, false, "Rethera", null, MatchMode.BEGINNING, namedAreas,
+ 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);
@SuppressWarnings("rawtypes")
- List<TaxonBase> results = taxonDao.findByNameTitleCache(true, false, includeUnpublished, "Rethera Rothschild & Jordan, 1903", null, MatchMode.EXACT, namedAreas,
+ 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");
@SuppressWarnings("rawtypes")
- List<TaxonBase> taxa = taxonDao.getTaxaByName(doTaxa, doSynonyms, noMisapplied, noCommonNames, false,"P", null, MatchMode.BEGINNING,
+ 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();
@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,
+ 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("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,
+ 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,
+ 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 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
BGBM BDI Projects / cdmlib.git / blobdiff