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);
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, subtree, 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, subtree, 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, subtree, 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, subtree, 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, subtree, 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);
@DataSet
public void testCountTaxaByName() {
TaxonNode subtree = null;
- long numberOfTaxa = taxonDao.countTaxaByName(true, false, false, false,false, "A", null, subtree, MatchMode.BEGINNING, null, includeUnpublished);
+ 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, subtree, 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, subtree, 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, subtree, 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, subtree, 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