2 * Copyright (C) 2009 EDIT
3 * European Distributed Institute of Taxonomy
4 * http://www.e-taxonomy.eu
6 * The contents of this file are subject to the Mozilla Public License Version 1.1
7 * See LICENSE.TXT at the top of this package for the full license terms.
10 package eu
.etaxonomy
.cdm
.persistence
.dao
.hibernate
.taxon
;
12 import static org
.junit
.Assert
.assertEquals
;
13 import static org
.junit
.Assert
.assertFalse
;
14 import static org
.junit
.Assert
.assertNotNull
;
15 import static org
.junit
.Assert
.assertNull
;
16 import static org
.junit
.Assert
.assertTrue
;
17 import static org
.junit
.Assert
.fail
;
19 import java
.io
.FileNotFoundException
;
20 import java
.util
.ArrayList
;
21 import java
.util
.HashSet
;
22 import java
.util
.List
;
24 import java
.util
.UUID
;
26 import org
.apache
.log4j
.Level
;
27 import org
.hibernate
.Hibernate
;
28 import org
.hibernate
.envers
.query
.AuditEntity
;
29 import org
.hibernate
.envers
.query
.criteria
.AuditCriterion
;
30 import org
.hibernate
.proxy
.HibernateProxy
;
31 import org
.junit
.After
;
32 import org
.junit
.Assert
;
33 import org
.junit
.Before
;
34 import org
.junit
.Test
;
35 import org
.unitils
.dbunit
.annotation
.DataSet
;
36 import org
.unitils
.dbunit
.annotation
.ExpectedDataSet
;
37 import org
.unitils
.spring
.annotation
.SpringBeanByType
;
39 import eu
.etaxonomy
.cdm
.hibernate
.HibernateProxyHelper
;
40 import eu
.etaxonomy
.cdm
.model
.common
.IdentifiableEntity
;
41 import eu
.etaxonomy
.cdm
.model
.common
.Marker
;
42 import eu
.etaxonomy
.cdm
.model
.common
.MarkerType
;
43 import eu
.etaxonomy
.cdm
.model
.location
.NamedArea
;
44 import eu
.etaxonomy
.cdm
.model
.name
.NonViralName
;
45 import eu
.etaxonomy
.cdm
.model
.name
.TaxonNameBase
;
46 import eu
.etaxonomy
.cdm
.model
.reference
.Reference
;
47 import eu
.etaxonomy
.cdm
.model
.taxon
.Classification
;
48 import eu
.etaxonomy
.cdm
.model
.taxon
.Synonym
;
49 import eu
.etaxonomy
.cdm
.model
.taxon
.SynonymType
;
50 import eu
.etaxonomy
.cdm
.model
.taxon
.Taxon
;
51 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonBase
;
52 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonNode
;
53 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonRelationship
;
54 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonRelationshipType
;
55 import eu
.etaxonomy
.cdm
.model
.view
.AuditEvent
;
56 import eu
.etaxonomy
.cdm
.model
.view
.AuditEventRecord
;
57 import eu
.etaxonomy
.cdm
.model
.view
.context
.AuditEventContextHolder
;
58 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.AuditEventSort
;
59 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.IDefinedTermDao
;
60 import eu
.etaxonomy
.cdm
.persistence
.dao
.reference
.IReferenceDao
;
61 import eu
.etaxonomy
.cdm
.persistence
.dao
.taxon
.IClassificationDao
;
62 import eu
.etaxonomy
.cdm
.persistence
.dao
.taxon
.ITaxonDao
;
63 import eu
.etaxonomy
.cdm
.persistence
.dto
.UuidAndTitleCache
;
64 import eu
.etaxonomy
.cdm
.persistence
.query
.GroupByCount
;
65 import eu
.etaxonomy
.cdm
.persistence
.query
.GroupByDate
;
66 import eu
.etaxonomy
.cdm
.persistence
.query
.Grouping
;
67 import eu
.etaxonomy
.cdm
.persistence
.query
.MatchMode
;
68 import eu
.etaxonomy
.cdm
.persistence
.query
.NativeSqlOrderHint
;
69 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
;
70 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
.SortOrder
;
71 import eu
.etaxonomy
.cdm
.test
.integration
.CdmTransactionalIntegrationTest
;
72 import eu
.etaxonomy
.cdm
.test
.unitils
.CleanSweepInsertLoadStrategy
;
78 public class TaxonDaoHibernateImplTest
extends CdmTransactionalIntegrationTest
{
81 private ITaxonDao taxonDao
;
84 private IClassificationDao classificationDao
;
87 private IReferenceDao referenceDao
;
90 IDefinedTermDao definedTermDao
;
93 private UUID sphingidae
;
94 private UUID acherontia
;
96 private UUID retheraSecCdmtest
;
97 private UUID atroposAgassiz
; // a Synonym
98 private UUID atroposLeach
; // a Synonym
99 private UUID acherontiaLachesis
;
101 private AuditEvent previousAuditEvent
;
102 private AuditEvent mostRecentAuditEvent
;
104 private UUID northernAmericaUuid
;
105 private UUID southernAmericaUuid
;
106 private UUID antarcticaUuid
;
108 private UUID classificationUuid
;
110 private static final String
[] TABLE_NAMES
= new String
[] {
111 "HOMOTYPICALGROUP", "HOMOTYPICALGROUP_AUD", "REFERENCE", "REFERENCE_AUD", "TAXONBASE", "TAXONBASE_AUD"
112 , "TAXONNAMEBASE", "TAXONNAMEBASE_AUD", "TAXONRELATIONSHIP", "TAXONRELATIONSHIP_AUD" };
116 public void setUp() {
118 uuid
= UUID
.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
119 sphingidae
= UUID
.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9");
120 acherontia
= UUID
.fromString("c5cc8674-4242-49a4-aada-72d63194f5fa");
121 acherontiaLachesis
= UUID
.fromString("b04cc9cb-2b4a-4cc4-a94a-3c93a2158b06");
122 atroposAgassiz
= UUID
.fromString("d75b2e3d-7394-4ada-b6a5-93175b8751c1");
123 atroposLeach
= UUID
.fromString("3da4ab34-6c50-4586-801e-732615899b07");
124 rethera
= UUID
.fromString("a9f42927-e507-4fda-9629-62073a908aae");
125 retheraSecCdmtest
= UUID
.fromString("a9f42927-e507-4fda-9629-62073a908aae");
127 previousAuditEvent
= new AuditEvent();
128 previousAuditEvent
.setRevisionNumber(1025);
129 previousAuditEvent
.setUuid(UUID
.fromString("a680fab4-365e-4765-b49e-768f2ee30cda"));
130 mostRecentAuditEvent
= new AuditEvent();
131 mostRecentAuditEvent
.setRevisionNumber(1026);
132 mostRecentAuditEvent
.setUuid(UUID
.fromString("afe8e761-8545-497b-9134-6a6791fc0b0d"));
133 AuditEventContextHolder
.clearContext(); // By default we're in the current view (i.e. view == null)
135 northernAmericaUuid
= UUID
.fromString("2757e726-d897-4546-93bd-7951d203bf6f");
136 southernAmericaUuid
= UUID
.fromString("6310b3ba-96f4-4855-bb5b-326e7af188ea");
137 antarcticaUuid
= UUID
.fromString("791b3aa0-54dd-4bed-9b68-56b4680aad0c");
139 classificationUuid
= UUID
.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9");
143 public void tearDown() {
144 AuditEventContextHolder
.clearContext();
148 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#TaxonDaoHibernateImpl()}.
152 public void testInit() {
153 logger
.warn("testInit()");
154 assertNotNull("Instance of ITaxonDao expected",taxonDao
);
155 assertNotNull("Instance of IReferenceDao expected",referenceDao
);
159 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
163 public void testGetTaxaByName() {
164 Reference sec
= referenceDao
.findById(1);
165 assert sec
!= null : "sec must exist";
167 List
<TaxonBase
> results
= taxonDao
.getTaxaByName("Aus", sec
);
168 assertNotNull("getTaxaByName should return a List", results
);
169 //assertFalse("The list should not be empty", results.isEmpty());
170 assertEquals(1, results
.size());
172 results
= taxonDao
.getTaxaByName("A*", MatchMode
.BEGINNING
, true, null, null);
173 assertNotNull("getTaxaByName should return a List", results
);
175 int numberOfTaxaByName_A
= 5;
177 logger
.setLevel(Level
.DEBUG
); //FIXME #######################
178 if (logger
.isDebugEnabled()) {
179 for (int i
= 0; i
< results
.size(); i
++) {
180 String nameCache
= "";
181 TaxonNameBase
<?
,?
> taxonNameBase
= results
.get(i
).getName();
182 nameCache
= HibernateProxyHelper
.deproxy(taxonNameBase
, NonViralName
.class).getNameCache();
183 logger
.debug(results
.get(i
).getClass() + "(" + i
+")" +
184 ": Name Cache = " + nameCache
+ ", Title Cache = " + results
.get(i
).getTitleCache());
188 assertEquals(numberOfTaxaByName_A
, results
.size());
191 //System.err.println("Species group: " + Rank.SPECIESGROUP().getId() + "Species: " + Rank.SPECIES().getId() + "Section Botany: "+ Rank.SECTION_BOTANY());
193 // assertEquals(results.get(0).getTitleCache(), "Abies sec. ???");
194 // assertEquals(results.get(1).getTitleCache(), "Abies Mill.");
195 // assertEquals(results.get(2).getTitleCache(), "Abies mill. sec. ???");
196 // assertEquals(results.get(3).getTitleCache(), "Abies alba sec. ???");
197 // assertEquals(results.get(4).getTitleCache(), "Abies alba Michx. sec. ???");
198 // assertEquals(results.get(5).getTitleCache(), "Abies alba Mill. sec. ???");
200 results
= taxonDao
.getTaxaByName("A*", MatchMode
.BEGINNING
, true, null, null);
201 assertNotNull("getTaxaByName should return a List", results
);
202 assertEquals(numberOfTaxaByName_A
, results
.size());
204 results
= taxonDao
.getTaxaByName("Aus", MatchMode
.EXACT
, true, null, null);
205 assertNotNull("getTaxaByName should return a List", results
);
206 assertEquals("Results list should contain one entity",1,results
.size());
211 @DataSet (loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
212 public void testGetTaxaByNameWithMisappliedNames(){
214 Classification classification
= classificationDao
.load(classificationUuid
);
217 * The testdata contains 3 misapplied names (1. nameCache = Aus, 2. nameCache = Rethera, 3. nameCache = Daphnis), two contained in the classification used in this test,
218 * the other one is not contained in any classification. This latter case is the more general situation.
219 * Misapplied names should be found regardless of whether they are contained in a classification or not.
221 //two accepted taxa starting with R in classification "TestBaum"
222 List
<TaxonBase
> results
= taxonDao
.getTaxaByName(true, false, false, "R*", classification
, MatchMode
.BEGINNING
, null, null, null, null);
223 Assert
.assertEquals("There should be 2 Taxa", 2, results
.size());
225 //three taxa, 2 accepted and 1 misapplied name starting with R
226 results
= taxonDao
.getTaxaByName(true, false, true, "R*", null, MatchMode
.BEGINNING
, null, null, null, null);
227 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
229 //one synonym has no accepted taxon
230 results
= taxonDao
.getTaxaByName(true, true, true, "A*", null, MatchMode
.BEGINNING
, null, null, null, null);
231 Assert
.assertEquals("There should be 11 Taxa",11, results
.size());
233 //two accepted taxa in classification and 1 misapplied name with accepted name in classification
234 results
= taxonDao
.getTaxaByName(true, true, true, "R*", classification
, MatchMode
.BEGINNING
, null, null, null, null);
235 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
237 //same as above because all taxa, synonyms and misapplied names starting with R are in the classification
238 results
= taxonDao
.getTaxaByName(true, true, true, "R*", null, MatchMode
.BEGINNING
, null, null, null, null);
239 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
241 //find misapplied names with accepted taxon in the classification, the accepted taxa of two misapplied names are in the classification
242 results
= taxonDao
.getTaxaByName(false, false, true, "*", classification
, MatchMode
.BEGINNING
, null, null, null, null);
243 Assert
.assertEquals("There should be 2 Taxa", 2, results
.size());
245 //find misapplied names beginning with R
246 results
= taxonDao
.getTaxaByName(false, false, true, "R*", null, MatchMode
.BEGINNING
, null, null, null, null);
247 Assert
.assertEquals("There should be 1 Taxa", 1, results
.size());
249 //find all three misapplied names
250 results
= taxonDao
.getTaxaByName(false, false, true, "*", null, MatchMode
.BEGINNING
, null, null, null, null);
251 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
256 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
260 public void testGetTaxaByNameForEditor() {
261 Reference sec
= referenceDao
.findById(1);
262 assert sec
!= null : "sec must exist";
264 List
<UuidAndTitleCache
<IdentifiableEntity
>> results
= taxonDao
.getTaxaByNameForEditor(true, true, false,false,"Acher", null, MatchMode
.BEGINNING
, null);
265 assertNotNull("getTaxaByName should return a List", results
);
266 assertFalse("The list should not be empty", results
.isEmpty());
267 assertEquals(4, results
.size());
270 results
= taxonDao
.getTaxaByNameForEditor(true, true, false, false,"A",null, MatchMode
.BEGINNING
, null);
271 assertNotNull("getTaxaByName should return a List", results
);
272 assertEquals(7, results
.size());
275 results
= taxonDao
.getTaxaByNameForEditor(true, false,false, false,"A", null,MatchMode
.BEGINNING
, null);
276 assertNotNull("getTaxaByName should return a List", results
);
277 assertEquals(5, results
.size());
278 assertEquals(results
.get(0).getType(), Taxon
.class);
280 results
= taxonDao
.getTaxaByNameForEditor(false, true,false,false, "A", null,MatchMode
.BEGINNING
, null);
281 assertNotNull("getTaxaByName should return a List", results
);
282 assertEquals(2, results
.size());
283 assertEquals(results
.get(0).getType(), Synonym
.class);
285 results
= taxonDao
.getTaxaByNameForEditor(true, true,false,false,"Aus", null,MatchMode
.EXACT
, null);
286 assertNotNull("getTaxaByName should return a List", results
);
287 assertEquals("Results list should contain one entity",1,results
.size());
289 results
= taxonDao
.getTaxaByNameForEditor(true, true,true,false,"A", null,MatchMode
.BEGINNING
, null);
290 assertNotNull("getTaxaByName should return a List", results
);
291 assertEquals("Results list should contain one entity", 8, results
.size());
293 //TODO: test the search for misapplied names
299 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}
300 * restricting the search by a set of Areas.
303 @DataSet(loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
304 public void testGetTaxaByNameAndArea() {
306 Set
<NamedArea
> namedAreas
= new HashSet
<NamedArea
>();
307 namedAreas
.add((NamedArea
)definedTermDao
.load(northernAmericaUuid
));
308 //namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
309 //namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
311 Classification taxonmicTree
= classificationDao
.findByUuid(classificationUuid
);
313 // prepare some synonym relation ships for some tests
314 Synonym synAtroposAgassiz
= (Synonym
)taxonDao
.findByUuid(atroposAgassiz
);
315 Taxon taxonRethera
= (Taxon
)taxonDao
.findByUuid(rethera
);
316 taxonRethera
.addSynonym(synAtroposAgassiz
, SynonymType
.SYNONYM_OF());
317 logger
.warn("addSynonym(..)");
319 Synonym synAtroposLeach
= (Synonym
)taxonDao
.findByUuid(atroposLeach
);
320 Taxon taxonRetheraSecCdmtest
= (Taxon
)taxonDao
.findByUuid(retheraSecCdmtest
);
321 taxonRetheraSecCdmtest
.addSynonym(synAtroposLeach
, SynonymType
.SYNONYM_OF());
322 this.taxonDao
.save(taxonRetheraSecCdmtest
);
324 Taxon test
= (Taxon
)this.taxonDao
.findByUuid(retheraSecCdmtest
);
325 // Set<Synonym> synonyms3 = test.getSynonyms();
326 // 1. searching for a taxon (Rethera)
327 //long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
329 List
<TaxonBase
> results
= taxonDao
.getTaxaByName(true,false, false, "Rethera", null, MatchMode
.BEGINNING
, namedAreas
,
331 assertNotNull("getTaxaByName should return a List", results
);
332 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 2);
334 // 2. searching for a taxon (Rethera) contained in a specific classification
335 results
= taxonDao
.getTaxaByName(true, false, false, "Rethera", taxonmicTree
, MatchMode
.BEGINNING
, namedAreas
,
337 assertNotNull("getTaxaByName should return a List", results
);
338 assertTrue("expected to find one taxon but found "+results
.size(), results
.size() == 1);
341 // 3. searching for Synonyms
342 results
= taxonDao
.getTaxaByName(false, true, false, "Atropo", null, MatchMode
.ANYWHERE
, null,
344 assertNotNull("getTaxaByName should return a List", results
);
345 /*System.err.println(results.get(0).getTitleCache() + " - " +results.get(1).getTitleCache() + " - " +results.get(2).getTitleCache() );
348 System.err.println(((Synonym)results.get(0)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(1)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(2)).getAcceptedTaxa().contains(taxonRethera)+ " - " );
350 assertTrue("expected to find three taxa but found "+results
.size(), results
.size() == 3);
352 // 4. searching for Synonyms
353 results
= taxonDao
.getTaxaByName(false, true, false, "Atropo", null, MatchMode
.BEGINNING
, null,
355 assertNotNull("getTaxaByName should return a List", results
);
356 assertTrue("expected to find three taxa but found "+results
.size(), results
.size() == 3);
359 // 5. searching for a Synonyms and Taxa
360 results
= taxonDao
.getTaxaByName(true, true, false, "A", null, MatchMode
.BEGINNING
, namedAreas
,
362 //only five taxa have a distribution
363 assertNotNull("getTaxaByName should return a List", results
);
364 assertTrue("expected to find 8 taxa but found "+results
.size(), results
.size() == 8);
369 * 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)}
370 * restricting the search by a set of Areas.
373 @DataSet(loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
374 public void testFindByNameTitleCache() {
376 Set
<NamedArea
> namedAreas
= new HashSet
<NamedArea
>();
377 namedAreas
.add((NamedArea
)definedTermDao
.load(northernAmericaUuid
));
378 //namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
379 //namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
381 Classification classification
= classificationDao
.findByUuid(classificationUuid
);
383 // prepare some synonym relation ships for some tests
384 Synonym synAtroposAgassiz
= (Synonym
)taxonDao
.findByUuid(atroposAgassiz
);
385 Taxon taxonRethera
= (Taxon
)taxonDao
.findByUuid(rethera
);
386 taxonRethera
.addSynonym(synAtroposAgassiz
, SynonymType
.SYNONYM_OF());
387 logger
.warn("addSynonym(..)");
388 this.taxonDao
.clear();
389 Synonym synAtroposLeach
= (Synonym
)taxonDao
.findByUuid(atroposLeach
);
390 Taxon taxonRetheraSecCdmtest
= (Taxon
)taxonDao
.findByUuid(retheraSecCdmtest
);
391 taxonRetheraSecCdmtest
.addSynonym(synAtroposLeach
, SynonymType
.SYNONYM_OF());
392 this.taxonDao
.clear();
393 // 1. searching for a taxon (Rethera)
394 //long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
396 List
<TaxonBase
> results
= taxonDao
.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", null, MatchMode
.EXACT
, namedAreas
,
398 assertNotNull("getTaxaByName should return a List", results
);
399 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 2);
401 // 2. searching for a taxon (Rethera) contained in a specific classification
402 results
= taxonDao
.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", classification
, MatchMode
.EXACT
, namedAreas
,
404 assertNotNull("getTaxaByName should return a List", results
);
405 assertTrue("expected to find one taxon but found "+results
.size(), results
.size() == 1);
408 // 3. searching for Synonyms
409 results
= taxonDao
.findByNameTitleCache(false, true, "*Atropo", null, MatchMode
.ANYWHERE
, null,
411 assertNotNull("getTaxaByName should return a List", results
);
413 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 2);
415 // 4. searching for Synonyms
416 results
= taxonDao
.findByNameTitleCache(false, true, "Atropo", null, MatchMode
.BEGINNING
, null,
418 assertNotNull("getTaxaByName should return a List", results
);
419 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 2);
422 // 5. searching for a Synonyms and Taxa
423 // attache a synonym first
424 Synonym syn
= (Synonym
)taxonDao
.findByUuid(this.atroposLeach
);
425 Taxon tax
= (Taxon
) taxonDao
.findByUuid(rethera
);
426 tax
.addSynonym(syn
, SynonymType
.HETEROTYPIC_SYNONYM_OF());
429 results
= taxonDao
.findByNameTitleCache(true, true, "A", null, MatchMode
.BEGINNING
, namedAreas
,
431 assertNotNull("getTaxaByName should return a List", results
);
432 assertTrue("expected to find 8 taxa but found "+results
.size(), results
.size() == 8);
436 @DataSet(loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
437 public void testTaxonNameInTwoClassifications(){
438 int numberOfClassifications
= classificationDao
.count();
439 List
<String
> propertyPaths
= new ArrayList
<String
>();
440 propertyPaths
.add("taxonNodes");
441 List
<TaxonBase
> taxa
= taxonDao
.getTaxaByName(true, true, false, "P", null, MatchMode
.BEGINNING
, null, null, null, null);
442 Taxon taxon
= (Taxon
)taxa
.get(0);
443 Set
<TaxonNode
> nodes
= taxon
.getTaxonNodes();
444 assertTrue(nodes
.size() == 1);
445 //assertNotNull(taxa);
446 //assertTrue(taxa.size() > 0);
451 public void testFindByUuid() {
452 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(uuid
);
453 assertNotNull("findByUuid should return a taxon",taxon
);
454 assertFalse("findByUuid should not return a taxon with it's name initialized",Hibernate
.isInitialized(taxon
.getName()));
459 public void testLoad() {
460 List
<String
> propertyPaths
= new ArrayList
<String
>();
461 propertyPaths
.add("name");
462 propertyPaths
.add("sec");
463 Taxon taxon
= (Taxon
)taxonDao
.load(uuid
, propertyPaths
);
464 assertNotNull("findByUuid should return a taxon",taxon
);
465 assertTrue("load should return a taxon with it's name initialized, given that the property was specified in the method",Hibernate
.isInitialized(taxon
.getName()));
466 assertTrue("load should return a taxon with it's secundum reference initialized, given that the property was specified in the method",Hibernate
.isInitialized(taxon
.getSec()));
471 public void testCountTaxonRelationshipsByTaxon() {
472 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
473 assert taxon
!= null : "taxon must exist";
475 int numberOfRelatedTaxa
= taxonDao
.countTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship
.Direction
.relatedTo
);
476 assertEquals("countTaxonRelationships should return 8", 8, numberOfRelatedTaxa
);
481 public void testCountTaxaByName() {
482 long numberOfTaxa
= taxonDao
.countTaxaByName(true, false, false, "A", null, MatchMode
.BEGINNING
, null);
483 assertEquals(5, numberOfTaxa
);
484 numberOfTaxa
= taxonDao
.countTaxaByName(true, false, false, "Smerinthus kindermannii", null, MatchMode
.EXACT
, null);
485 assertEquals(1, numberOfTaxa
);
486 numberOfTaxa
= taxonDao
.countTaxaByName(false, true, false, "A", null, MatchMode
.BEGINNING
, null);
487 assertEquals(2, numberOfTaxa
);
488 numberOfTaxa
= taxonDao
.countTaxaByName(true, true, false, "A", null, MatchMode
.BEGINNING
, null);
489 assertEquals(7, numberOfTaxa
);
490 numberOfTaxa
= taxonDao
.countTaxaByName(true, true, false, "Aasfwerfwf fffe", null, MatchMode
.BEGINNING
, null);
491 assertEquals(0, numberOfTaxa
);
492 // FIXME implement test for search in specific classification
493 // Reference reference = referenceDao.findByUuid(UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2"));
494 // numberOfTaxa = taxonDao.countTaxaByName("A*", MatchMode.BEGINNING, SelectMode.ALL, null, null);
495 // assertEquals(numberOfTaxa, 2);
500 public void testRelatedTaxa() {
501 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
502 assert taxon
!= null : "taxon must exist";
504 List
<String
> propertyPaths
= new ArrayList
<String
>();
505 propertyPaths
.add("fromTaxon");
506 propertyPaths
.add("fromTaxon.name");
507 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
508 orderHints
.add(new OrderHint("relatedFrom.name.genusOrUninomial", SortOrder
.ASCENDING
));
509 orderHints
.add(new OrderHint("relatedFrom.name.specificEpithet", SortOrder
.ASCENDING
));
510 orderHints
.add(new OrderHint("relatedFrom.name.infraSpecificEpithet", SortOrder
.ASCENDING
));
512 List
<TaxonRelationship
> relatedTaxa
= taxonDao
.getTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), null, null, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
513 assertNotNull("getRelatedTaxa should return a List",relatedTaxa
);
514 assertEquals("getRelatedTaxa should return all 8 related taxa", 8, relatedTaxa
.size());
515 assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate
.isInitialized(relatedTaxa
.get(0).getFromTaxon()));
516 assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate
.isInitialized(relatedTaxa
.get(0).getFromTaxon().getName()));
518 assertEquals("Acherontia should appear first in the list of related taxa", relatedTaxa
.get(0).getFromTaxon().getTitleCache(), "Acherontia Laspeyres, 1809 sec. cate-sphingidae.org");
519 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());
524 public void testGetRelatedTaxaPaged() {
525 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
526 assert taxon
!= null : "taxon must exist";
528 List
<String
> propertyPaths
= new ArrayList
<String
>();
529 propertyPaths
.add("fromTaxon");
530 propertyPaths
.add("fromTaxon.name");
532 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
533 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
536 List
<TaxonRelationship
> firstPage
= taxonDao
.getTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), pageSize
, 0, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
537 List
<TaxonRelationship
> secondPage
= taxonDao
.getTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(),pageSize
, 1, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
538 List
<TaxonRelationship
> thirdPage
= taxonDao
.getTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), pageSize
, 2, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
540 assertNotNull("getRelatedTaxa: 3, 0 should return a List",firstPage
);
541 assertEquals("getRelatedTaxa: 3, 0 should return a List with 3 elements", pageSize
,firstPage
.size());
542 assertNotNull("getRelatedTaxa: 3, 1 should return a List",secondPage
);
543 assertEquals("getRelatedTaxa: 3, 1 should return a List with 3 elements", pageSize
, secondPage
.size());
544 assertNotNull("getRelatedTaxa: 3, 2 should return a List",thirdPage
);
545 assertEquals("getRelatedTaxa: 3, 2 should return a List with 2 elements", 2, thirdPage
.size());
550 public void testCountSynonyms() {
551 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
552 assert taxon
!= null : "taxon must exist";
554 int numberOfRelatedSynonym
= taxonDao
.countSynonyms(taxon
,null);
555 assertEquals("countSynonyms should return 3", 3, numberOfRelatedSynonym
);
560 public void testGetSynonyms() {
561 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
562 assert taxon
!= null : "taxon must exist";
563 List
<String
> propertyPaths
= new ArrayList
<String
>();
564 propertyPaths
.add("synonym");
565 propertyPaths
.add("synonym.name");
567 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
568 orderHints
.add(new OrderHint("titleCache", SortOrder
.ASCENDING
));
570 List
<Synonym
> synonyms
= taxonDao
.getSynonyms(taxon
, null, null, null,orderHints
,propertyPaths
);
572 assertNotNull("getSynonyms should return a List", synonyms
);
573 assertEquals("getSynonyms should return 3 synonyms", 3, synonyms
.size());
574 assertTrue("getSynonyms should return synonym objects with the synonym initialized", Hibernate
.isInitialized(synonyms
.get(0)));
579 public void testCountSynonymsByType() {
580 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
581 assert taxon
!= null : "taxon must exist";
583 int numberOfTaxonomicSynonyms
= taxonDao
.countSynonyms(taxon
, SynonymType
.HETEROTYPIC_SYNONYM_OF());
584 assertEquals("countSynonyms should return 4", 3, numberOfTaxonomicSynonyms
);
589 public void testSynonymsByType() {
590 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
591 assert taxon
!= null : "taxon must exist";
593 List
<Synonym
> synonyms
= taxonDao
.getSynonyms(taxon
, SynonymType
.HETEROTYPIC_SYNONYM_OF(), null, null,null,null);
595 assertNotNull("getSynonyms should return a List", synonyms
);
596 assertEquals("getSynonyms should return 4 Synonyms", 3, synonyms
.size());
601 public void testPageSynonyms(){
602 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
603 assert taxon
!= null : "taxon must exist";
606 List
<Synonym
> firstPage
= taxonDao
.getSynonyms(taxon
, null, pageSize
, 0,null,null);
607 List
<Synonym
> secondPage
= taxonDao
.getSynonyms(taxon
, null, pageSize
, 1,null,null);
609 assertNotNull("getSynonyms: 2, 0 should return a List",firstPage
);
610 assertEquals("getSynonyms: 2, 0 should return 2 synonyms", pageSize
,firstPage
.size());
611 assertNotNull("getSynonyms: 2, 1 should return a List",secondPage
);
612 assertEquals("getSynonyms: 2, 1 should return 1 synonym", 1, secondPage
.size());
617 public void testCountTaxonRelationships() {
618 long count
= taxonDao
.countTaxonRelationships(null);
619 assertEquals("There should be 11 relationships", 11, count
);
621 Set
<TaxonRelationshipType
> types
= new HashSet
<>();
622 count
= taxonDao
.countTaxonRelationships(types
);
623 assertEquals("Empty filter should return empty result", 0, count
);
625 types
.add(TaxonRelationshipType
.CONGRUENT_TO());
626 count
= taxonDao
.countTaxonRelationships(types
);
627 assertEquals("There should be no congruent relationship", 0, count
);
629 types
.add(TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN());
630 count
= taxonDao
.countTaxonRelationships(types
);
631 assertEquals("There should be 11 tax included relationships", 11, count
);
636 public void testlistTaxonRelationships() {
637 List
<TaxonRelationship
> rels
= taxonDao
.getTaxonRelationships(null, null, null, null, null);
638 assertEquals("There should be 11 relationships", 11, rels
.size());
640 rels
= taxonDao
.getTaxonRelationships(null, 2, 3, null, null);
641 assertEquals("There should be 11 relationships", 2, rels
.size());
643 Set
<TaxonRelationshipType
> types
= new HashSet
<>();
644 rels
= taxonDao
.getTaxonRelationships(types
, null, null, null, null);
645 assertEquals("Empty filter should return empty result", 0, rels
.size());
647 types
.add(TaxonRelationshipType
.CONGRUENT_TO());
648 rels
= taxonDao
.getTaxonRelationships(types
, null, null, null, null);
649 assertEquals("There should be no congruent relationship", 0, rels
.size());
651 types
.add(TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN());
652 rels
= taxonDao
.getTaxonRelationships(types
, null, null, null, null);
653 assertEquals("There should be 11 tax included relationships", 11, rels
.size());
657 @DataSet("TaxonNodeDaoHibernateImplTest.xml")
658 public void testListAcceptedTaxaFor() {
659 UUID acheontitia_ciprosus
= UUID
.fromString("3ef145f7-bd92-4a64-8afd-2b8203e00e02");
661 Synonym synonym
= (Synonym
)taxonDao
.findByUuid(acheontitia_ciprosus
);
662 assertNotNull("synonym must exist", synonym
);
664 Taxon taxon
= taxonDao
.acceptedTaxonFor(synonym
, null, null);
665 assertNotNull("listAcceptedTaxaFor should return a taxon", taxon
);
667 Classification classification
= classificationDao
.load(classificationUuid
);
668 assertNotNull("classification must exist", classification
);
670 taxon
= taxonDao
.acceptedTaxonFor(synonym
, classification
, null);
671 assertNull("listAcceptedTaxaFor should return not taxon due to classification filter", taxon
);
677 public void testGetTaxonMatchingUninomial() {
678 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class, "Smerinthus", "*", "*", "*","*",null,null,null);
680 assertNotNull("findTaxaByName should return a List", result
);
681 assertEquals("findTaxaByName should return two Taxa",2,result
.size());
682 assertEquals("findTaxaByName should return a Taxon with id 5",5,result
.get(0).getId());
687 public void testGetTaxonMatchingSpeciesBinomial() {
688 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class, "Smerinthus", null, "kindermannii", null,"*",null,null,null);
690 assertNotNull("findTaxaByName should return a List", result
);
691 assertEquals("findTaxaByName should return one Taxon",1,result
.size());
692 assertEquals("findTaxaByName should return a Taxon with id 8",8,result
.get(0).getId());
697 public void testGetTaxonMatchingTrinomial() {
698 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class,"Cryptocoryne", null,"purpurea","borneoensis","*",null,null,null);
700 assertNotNull("findTaxaByName should return a List", result
);
701 assertEquals("findTaxaByName should return one Taxon",1,result
.size());
702 assertEquals("findTaxaByName should return a Taxon with id 38",38,result
.get(0).getId());
707 public void testNegativeMatch() {
708 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class,"Acherontia", null,"atropos","dehli",null,null,null,null);
710 assertNotNull("findTaxaByName should return a List", result
);
711 assertTrue("findTaxaByName should return an empty List",result
.isEmpty());
716 public void testCountAllTaxa() {
717 int numberOfTaxa
= taxonDao
.count(Taxon
.class);
718 assertEquals("count should return 14 taxa", 14, numberOfTaxa
);
723 public void testListAllTaxa() {
724 List
<Taxon
> taxa
= taxonDao
.list(Taxon
.class,100, 0);
725 assertNotNull("list should return a List", taxa
);
726 assertEquals("list should return 14 taxa", 14, taxa
.size());
732 public void testDelete() {
733 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
734 assert taxon
!= null : "taxon must exist";
735 taxonDao
.delete(taxon
);
736 taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
737 assert taxon
== null : "taxon must not exist";
741 // printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
742 // } catch (FileNotFoundException e) {
743 // e.printStackTrace();
749 @ExpectedDataSet("TaxonDaoHibernateImplTest.testDelete-result.xml")
750 public void testDeleteWithMarker() {
751 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
752 taxon
.addMarker(Marker
.NewInstance(MarkerType
.IS_DOUBTFUL(), true));
753 taxonDao
.save(taxon
);
754 assert taxon
!= null : "taxon must exist";
756 taxonDao
.delete(taxon
);
757 commitAndStartNewTransaction(null);
758 taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
759 assert taxon
== null : "taxon must not exist";
763 // printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES);
764 // } catch (FileNotFoundException e) {
765 // e.printStackTrace();
770 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
771 public void testFindDeleted() {
772 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(acherontia
);
773 assertNull("findByUuid should return null in this view", taxon
);
774 assertFalse("exist should return false in this view",taxonDao
.exists(acherontia
));
778 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
779 public void testFindDeletedInPreviousView() {
780 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
781 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
782 assertNotNull("findByUuid should return a taxon in this view",taxon
);
783 assertTrue("exists should return true in this view", taxonDao
.exists(acherontia
));
786 assertEquals("There should be 3 relations to this taxon in this view",3,taxon
.getRelationsToThisTaxon().size());
787 } catch(Exception e
) {
788 fail("We should not experience any problems initializing proxies with envers");
793 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
794 public void testGetAuditEvents() {
795 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
796 assert taxon
!= null : "taxon cannot be null";
798 List
<String
> propertyPaths
= new ArrayList
<String
>();
799 propertyPaths
.add("name");
800 propertyPaths
.add("createdBy");
801 propertyPaths
.add("updatedBy");
803 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(taxon
, null,null,null,propertyPaths
);
804 assertNotNull("getAuditEvents should return a list",auditEvents
);
805 assertFalse("the list should not be empty",auditEvents
.isEmpty());
806 assertEquals("There should be two AuditEventRecords in the list",2, auditEvents
.size());
810 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
811 public void testGetAuditEventsFromNow() {
812 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
813 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
814 assert taxon
!= null : "taxon cannot be null";
816 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(taxon
, null,null,AuditEventSort
.FORWARDS
,null);
817 assertNotNull("getAuditEvents should return a list",auditEvents
);
818 assertFalse("the list should not be empty",auditEvents
.isEmpty());
819 assertEquals("There should be one audit event in the list",1,auditEvents
.size());
823 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
824 public void testCountAuditEvents() {
825 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
826 assert taxon
!= null : "taxon cannot be null";
828 int numberOfAuditEvents
= taxonDao
.countAuditEvents(taxon
,null);
829 assertEquals("countAuditEvents should return 2",numberOfAuditEvents
,2);
833 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
834 public void getPreviousAuditEvent() {
835 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
836 assert taxon
!= null : "taxon cannot be null";
838 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getPreviousAuditEvent(taxon
);
839 assertNotNull("getPreviousAuditEvent should not return null as there is at least one audit event prior to the current one",auditEvent
);
843 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
844 public void getPreviousAuditEventAtBeginning() {
845 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
846 TaxonBase taxon
= taxonDao
.findByUuid(sphingidae
);
847 assert taxon
!= null : "taxon cannot be null";
849 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getPreviousAuditEvent(taxon
);
850 assertNull("getPreviousAuditEvent should return null if we're at the first audit event anyway",auditEvent
);
854 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
855 public void getNextAuditEvent() {
856 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
857 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
858 assert taxon
!= null : "taxon cannot be null";
860 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getNextAuditEvent(taxon
);
861 assertNotNull("getNextAuditEvent should not return null as there is at least one audit event after the current one",auditEvent
);
865 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
866 public void getNextAuditEventAtEnd() {
867 AuditEventContextHolder
.getContext().setAuditEvent(mostRecentAuditEvent
);
868 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
869 assert taxon
!= null : "taxon cannot be null";
871 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getNextAuditEvent(taxon
);
872 assertNull("getNextAuditEvent should return null as there no more audit events after the current one",auditEvent
);
876 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
877 public void testFind() {
878 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
879 assert taxon
!= null : "taxon cannot be null";
881 assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon
.getRelationsToThisTaxon().size());
885 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
886 public void testFindInPreviousView() {
887 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
888 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
889 assert taxon
!= null : "taxon cannot be null";
891 assertTrue("getRelationsToThisTaxon should contain 0 TaxonRelationship in this view",taxon
.getRelationsToThisTaxon().isEmpty());
895 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
896 public void testGetRelations() {
897 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
898 assert taxon
!= null : "taxon cannot be null";
900 List
<String
> propertyPaths
= new ArrayList
<String
>();
901 propertyPaths
.add("fromTaxon");
902 propertyPaths
.add("fromTaxon.name");
904 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
905 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
907 List
<TaxonRelationship
> taxonRelations
= taxonDao
.getTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedFrom
);
908 assertNotNull("getRelatedTaxa should return a list", taxonRelations
);
909 assertEquals("there should be one TaxonRelationship in the list in the current view",1,taxonRelations
.size());
910 assertTrue("TaxonRelationship.relatedFrom should be initialized",Hibernate
.isInitialized(taxonRelations
.get(0).getFromTaxon()));
911 assertTrue("TaxonRelationship.relatedFrom.name should be initialized",Hibernate
.isInitialized(taxonRelations
.get(0).getFromTaxon().getName()));
915 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
916 public void testCountRelations() {
917 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
918 assert taxon
!= null : "taxon cannot be null";
919 assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao
.countTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship
.Direction
.relatedTo
));
923 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
924 public void testGetRelationsInPreviousView() {
925 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
926 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
927 assert taxon
!= null : "taxon cannot be null";
929 List
<String
> propertyPaths
= new ArrayList
<String
>();
930 propertyPaths
.add("relatedFrom");
931 propertyPaths
.add("relatedFrom.name");
933 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
934 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
936 List
<TaxonRelationship
> taxonRelations
= taxonDao
.getTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedFrom
);
937 assertNotNull("getRelatedTaxa should return a list",taxonRelations
);
938 assertTrue("there should be no TaxonRelationships in the list in the prior view",taxonRelations
.isEmpty());
942 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
943 public void testCountRelationsInPreviousView() {
944 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
945 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
946 assert taxon
!= null : "taxon cannot be null";
947 assertEquals("countRelatedTaxa should return 0 in the current view",0, taxonDao
.countTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship
.Direction
.relatedTo
));
952 public void testGroupTaxa() {
953 List
<Grouping
> groups
= new ArrayList
<Grouping
>();
954 groups
.add(new GroupByCount("count",SortOrder
.DESCENDING
));
955 groups
.add(new Grouping("name.genusOrUninomial", "genus", "n", SortOrder
.ASCENDING
));
956 List
<Object
[]> results
= taxonDao
.group(null, null, null, groups
,null);
957 System
.out
.println("count\tname.genuOrUninomial");
958 for(Object
[] result
: results
) {
959 System
.out
.println(result
[0] + "\t" + result
[1]);
965 public void testGroupTaxaByClass() {
966 List
<Grouping
> groups
= new ArrayList
<Grouping
>();
967 groups
.add(new GroupByCount("count",SortOrder
.DESCENDING
));
968 groups
.add(new Grouping("class", "class",null, SortOrder
.ASCENDING
));
969 List
<Object
[]> results
= taxonDao
.group(null, null, null, groups
,null);
970 System
.out
.println("count\tclass");
971 for(Object
[] result
: results
) {
972 System
.out
.println(result
[0] + "\t" + result
[1]);
978 public void testNativeSQLOrder() {
979 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
980 orderHints
.add(new NativeSqlOrderHint("case when {alias}.titleCache like 'C%' then 0 else 1 end",SortOrder
.ASCENDING
));
982 List
<TaxonBase
> results
= taxonDao
.list(null, null, orderHints
);
983 System
.out
.println("native SQL order");
984 for(TaxonBase
<?
> result
: results
) {
985 System
.out
.println(result
.getTitleCache());
991 public void testGroupByDateTaxa() {
992 List
<Grouping
> groups
= new ArrayList
<Grouping
>();
993 groups
.add(new GroupByCount("count",null));
994 groups
.add(new GroupByDate("created", "dateGroup", SortOrder
.ASCENDING
, GroupByDate
.Resolution
.MONTH
));
995 List
<Object
[]> results
= taxonDao
.group(null, null, null, groups
,null);
996 System
.out
.println("count\tyear\tmonth");
997 for(Object
[] result
: results
) {
998 System
.out
.println(result
[0] + "\t" + result
[1] + "\t" + result
[2]);
1003 @DataSet ("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
1004 public final void testGetTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(){
1005 Classification classification
= classificationDao
.findByUuid(classificationUuid
);
1006 List
<UuidAndTitleCache
<TaxonNode
>> result
= taxonDao
.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification
, null, null);
1007 assertNotNull(result
);
1008 assertEquals(5, result
.size());
1011 UUID excludeUUID
= UUID
.fromString("a9f42927-e507-4fda-9629-62073a908aae");
1012 List
<UUID
> excludeUUids
= new ArrayList
<UUID
>();
1013 excludeUUids
.add(excludeUUID
);
1014 result
= taxonDao
.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification
, null, null);
1015 assertEquals(5, result
.size());
1019 result
= taxonDao
.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification
, limit
, null);
1020 assertEquals(2, result
.size());
1023 String pattern
= "*Rothschi*";
1024 result
= taxonDao
.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification
, 2, pattern
);
1025 assertNotNull(result
);
1026 assertEquals(1, result
.size());
1027 assertEquals("0b5846e5-b8d2-4ca9-ac51-099286ea4adc", result
.get(0).getUuid().toString());
1033 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
1034 //NOTE: There is a problem with loading AuditEvents if this test runs
1035 //stand alone or as first (one of the first) in the test suite. For some reason
1036 //the AuditEvent records from the @DataSet are not inserted into the database then,
1037 //while those inserted by the terms dataset are inserted as well as a completely new one.
1038 //This problem for some reason does not happen if not running at first place
1039 public void testGetAuditEventsByTypeWithRestrictions() {
1040 commitAndStartNewTransaction(new String
[]{"AUDITEVENT", "TAXONBASE_AUD"});
1042 List
<String
> propertyPaths
= new ArrayList
<String
>();
1043 propertyPaths
.add("name");
1044 propertyPaths
.add("createdBy");
1045 propertyPaths
.add("updatedBy");
1047 List
<AuditCriterion
> criteria
= new ArrayList
<AuditCriterion
>();
1048 criteria
.add(AuditEntity
.property("lsid_lsid").isNotNull());
1050 int count
= taxonDao
.countAuditEvents(TaxonBase
.class, null, null, null);
1052 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(TaxonBase
.class, previousAuditEvent
, mostRecentAuditEvent
, criteria
,null, null, AuditEventSort
.FORWARDS
, propertyPaths
);
1053 assertNotNull("getAuditEvents should return a list",auditEvents
);
1054 assertFalse("the list should not be empty",auditEvents
.isEmpty());
1055 assertEquals("There should be one AuditEventRecord in the list",1, auditEvents
.size());
1060 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
1061 // @DataSets({ //for testing only
1062 // @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml"),
1063 // @DataSet("TaxonDaoHibernateImplTest.testFindDeletedAuditEvents.xml")
1065 //NOTE: There is a problem with loading AuditEvents if this test runs
1066 //stand alone or as first (one of the first) in the test suite. For some reason
1067 //the AuditEvent records from the @DataSet are not inserted into the database then,
1068 //while those inserted by the terms dataset are inserted as well as a completely new one.
1069 //This problem for some reason does not happen if not running at first place
1070 public void testGetAuditEventsByTypeWithNoRestrictions() {
1071 printDataSet(System
.out
, new String
[]{"AUDITEVENT", "TAXONBASE_AUD"});
1072 commitAndStartNewTransaction(new String
[]{"AUDITEVENT", "TAXONBASE_AUD"});
1074 List
<String
> propertyPaths
= new ArrayList
<String
>();
1075 propertyPaths
.add("name");
1076 propertyPaths
.add("createdBy");
1077 propertyPaths
.add("updatedBy");
1078 int count
= taxonDao
.countAuditEvents(TaxonBase
.class, null, null, null);
1079 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(TaxonBase
.class, previousAuditEvent
, mostRecentAuditEvent
, null,null, null, AuditEventSort
.FORWARDS
, propertyPaths
);
1080 assertNotNull("getAuditEvents should return a list", auditEvents
);
1081 assertFalse("the list should not be empty", auditEvents
.isEmpty());
1082 assertEquals("There should be thirty eight AuditEventRecords in the list", 2, auditEvents
.size());
1087 @DataSet("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
1088 public void testGetCommonName(){
1089 List
<Taxon
> commonNameResults
= taxonDao
.getTaxaByCommonName("common%", null,
1090 MatchMode
.BEGINNING
, null, null, null, null);
1092 assertNotNull("getTaxaByCommonName should return a list", commonNameResults
);
1093 assertFalse("the list should not be empty", commonNameResults
.isEmpty());
1094 assertEquals("There should be one Taxon with common name", 1,commonNameResults
.size());
1095 assertEquals(" sec. ???", ((TaxonBase
)commonNameResults
.get(0)).getTitleCache());
1100 public void testGetTitleCache(){
1101 UUID uuid
= UUID
.fromString("7b8b5cb3-37ba-4dba-91ac-4c6ffd6ac331");
1102 String titleCache
= taxonDao
.getTitleCache(uuid
, false);
1103 Assert
.assertEquals("Acherontia styx Westwood, 1847 sec. cate-sphingidae.org", titleCache
);
1104 titleCache
= taxonDao
.getTitleCache(uuid
, true);
1105 Assert
.assertEquals("Acherontia styxx Westwood, 1847 sec. cate-sphingidae.org", titleCache
);
1110 @DataSet("TaxonDaoHibernateImplTest.testPropertyPath.xml")
1111 public void testPropertyPath(){
1112 //Test that BeanInitializer also works on HiberanteProxys
1113 Classification c
= classificationDao
.load(UUID
.fromString("4bceea53-893f-4685-8c63-6dcec6e85ab1"));
1114 TaxonNode singleNode
= c
.getRootNode().getChildNodes().iterator().next();
1115 Taxon taxonProxy
= singleNode
.getTaxon();
1116 Assert
.assertTrue("Object to test should be a proxy ", taxonProxy
instanceof HibernateProxy
);
1118 List
<String
> propertyPaths
= new ArrayList
<String
>();
1119 propertyPaths
.add("taxonNodes");
1120 Taxon taxon
= (Taxon
)this.taxonDao
.load(
1121 UUID
.fromString("4a5bc930-844f-45ec-aea8-dd155e1ab25f"),
1123 Assert
.assertSame("Returned object should be the same proxy to assure that we ran initialization on this proxy", taxonProxy
, taxon
);
1131 public void createTestDataSet() throws FileNotFoundException
{
1132 // Classification classification = Classification.NewInstance("Test");
1133 // BotanicalName taxonNameBase = null;
1134 // Reference sec = null;
1135 // Taxon taxon = Taxon.NewInstance(taxonNameBase, sec);
1136 // classification.addChildTaxon(taxon, sec, null);
1138 // classificationDao.save(classification);
1139 // this.commitAndStartNewTransaction(null);
1141 // writeDbUnitDataSetFile(new String[] {
1142 // "CLASSIFICATION", "TAXONNAMEBASE",
1143 // "REFERENCE","TAXONNODE",
1144 // "TAXONBASE","LANGUAGESTRING",
1145 // "HIBERNATE_SEQUENCES" // IMPORTANT!!!
1147 // "testPropertyPath" );