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
.assertSame
;
16 import static org
.junit
.Assert
.assertTrue
;
17 import static org
.junit
.Assert
.assertNull
;
18 import static org
.junit
.Assert
.fail
;
20 import java
.io
.FileNotFoundException
;
21 import java
.io
.FileOutputStream
;
22 import java
.util
.ArrayList
;
23 import java
.util
.HashSet
;
24 import java
.util
.List
;
26 import java
.util
.UUID
;
28 import org
.junit
.Assert
;
30 import org
.apache
.log4j
.Level
;
31 import org
.hibernate
.Hibernate
;
32 import org
.hibernate
.envers
.query
.AuditEntity
;
33 import org
.hibernate
.envers
.query
.criteria
.AuditCriterion
;
34 import org
.junit
.After
;
35 import org
.junit
.Before
;
36 import org
.junit
.Ignore
;
37 import org
.junit
.Test
;
38 import org
.unitils
.dbunit
.annotation
.DataSet
;
39 import org
.unitils
.dbunit
.annotation
.ExpectedDataSet
;
40 import org
.unitils
.spring
.annotation
.SpringBeanByType
;
42 import eu
.etaxonomy
.cdm
.hibernate
.HibernateProxyHelper
;
43 import eu
.etaxonomy
.cdm
.model
.common
.UuidAndTitleCache
;
44 import eu
.etaxonomy
.cdm
.model
.location
.NamedArea
;
45 import eu
.etaxonomy
.cdm
.model
.name
.NonViralName
;
46 import eu
.etaxonomy
.cdm
.model
.name
.Rank
;
47 import eu
.etaxonomy
.cdm
.model
.name
.TaxonNameBase
;
48 import eu
.etaxonomy
.cdm
.model
.reference
.Reference
;
49 import eu
.etaxonomy
.cdm
.model
.taxon
.Classification
;
50 import eu
.etaxonomy
.cdm
.model
.taxon
.Synonym
;
51 import eu
.etaxonomy
.cdm
.model
.taxon
.SynonymRelationship
;
52 import eu
.etaxonomy
.cdm
.model
.taxon
.SynonymRelationshipType
;
53 import eu
.etaxonomy
.cdm
.model
.taxon
.Taxon
;
54 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonBase
;
55 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonNode
;
56 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonRelationship
;
57 import eu
.etaxonomy
.cdm
.model
.taxon
.TaxonRelationshipType
;
58 import eu
.etaxonomy
.cdm
.model
.view
.AuditEvent
;
59 import eu
.etaxonomy
.cdm
.model
.view
.AuditEventRecord
;
60 import eu
.etaxonomy
.cdm
.model
.view
.context
.AuditEventContextHolder
;
61 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.AuditEventSort
;
62 import eu
.etaxonomy
.cdm
.persistence
.dao
.common
.IDefinedTermDao
;
63 import eu
.etaxonomy
.cdm
.persistence
.dao
.reference
.IReferenceDao
;
64 import eu
.etaxonomy
.cdm
.persistence
.dao
.taxon
.IClassificationDao
;
65 import eu
.etaxonomy
.cdm
.persistence
.dao
.taxon
.ITaxonDao
;
66 import eu
.etaxonomy
.cdm
.persistence
.fetch
.CdmFetch
;
67 import eu
.etaxonomy
.cdm
.persistence
.query
.GroupByCount
;
68 import eu
.etaxonomy
.cdm
.persistence
.query
.GroupByDate
;
69 import eu
.etaxonomy
.cdm
.persistence
.query
.Grouping
;
70 import eu
.etaxonomy
.cdm
.persistence
.query
.MatchMode
;
71 import eu
.etaxonomy
.cdm
.persistence
.query
.NativeSqlOrderHint
;
72 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
;
73 import eu
.etaxonomy
.cdm
.persistence
.query
.OrderHint
.SortOrder
;
74 import eu
.etaxonomy
.cdm
.test
.integration
.CdmTransactionalIntegrationTest
;
75 import eu
.etaxonomy
.cdm
.test
.unitils
.CleanSweepInsertLoadStrategy
;
82 @Ignore //FIXME running out of time, so I hope someone else can fix the testdata for this class (Andreas Kohlbecker)
83 public class TaxonDaoHibernateImplTest
extends CdmTransactionalIntegrationTest
{
86 private ITaxonDao taxonDao
;
89 private IClassificationDao classificationDao
;
92 private IReferenceDao referenceDao
;
95 IDefinedTermDao definedTermDao
;
98 private UUID sphingidae
;
99 private UUID acherontia
;
101 private UUID rethera
;
102 private UUID retheraSecCdmtest
;
103 private UUID atroposAgassiz
;
104 private UUID atroposLeach
;
105 private UUID acherontiaLachesis
;
106 private AuditEvent previousAuditEvent
;
107 private AuditEvent mostRecentAuditEvent
;
109 private UUID northernAmericaUuid
;
110 private UUID southernAmericaUuid
;
111 private UUID antarcticaUuid
;
113 private UUID classificationUuid
;
115 private static final String
[] TABLE_NAMES
= new String
[] {
116 "HOMOTYPICALGROUP", "HOMOTYPICALGROUP_AUD", "REFERENCE", "REFERENCE_AUD", "SYNONYMRELATIONSHIP", "SYNONYMRELATIONSHIP_AUD", "TAXONBASE", "TAXONBASE_AUD"
117 , "TAXONNAMEBASE", "TAXONNAMEBASE_AUD", "TAXONRELATIONSHIP", "TAXONRELATIONSHIP_AUD" };
121 public void setUp() {
123 uuid
= UUID
.fromString("496b1325-be50-4b0a-9aa2-3ecd610215f2");
124 sphingidae
= UUID
.fromString("54e767ee-894e-4540-a758-f906ecb4e2d9");
125 acherontia
= UUID
.fromString("c5cc8674-4242-49a4-aada-72d63194f5fa");
126 acherontiaLachesis
= UUID
.fromString("b04cc9cb-2b4a-4cc4-a94a-3c93a2158b06");
127 atroposAgassiz
= UUID
.fromString("d75b2e3d-7394-4ada-b6a5-93175b8751c1");
128 atroposLeach
= UUID
.fromString("3da4ab34-6c50-4586-801e-732615899b07");
129 rethera
= UUID
.fromString("a9f42927-e507-4fda-9629-62073a908aae");
130 retheraSecCdmtest
= UUID
.fromString("a9f42927-e507-4fda-9629-62073a908aae");
133 mimas
= UUID
.fromString("900052b7-b69c-4e26-a8f0-01c215214c40");
134 previousAuditEvent
= new AuditEvent();
135 previousAuditEvent
.setRevisionNumber(1025);
136 previousAuditEvent
.setUuid(UUID
.fromString("a680fab4-365e-4765-b49e-768f2ee30cda"));
137 mostRecentAuditEvent
= new AuditEvent();
138 mostRecentAuditEvent
.setRevisionNumber(1026);
139 mostRecentAuditEvent
.setUuid(UUID
.fromString("afe8e761-8545-497b-9134-6a6791fc0b0d"));
140 AuditEventContextHolder
.clearContext(); // By default we're in the current view (i.e. view == null)
142 northernAmericaUuid
= UUID
.fromString("2757e726-d897-4546-93bd-7951d203bf6f");
143 southernAmericaUuid
= UUID
.fromString("6310b3ba-96f4-4855-bb5b-326e7af188ea");
144 antarcticaUuid
= UUID
.fromString("791b3aa0-54dd-4bed-9b68-56b4680aad0c");
146 classificationUuid
= UUID
.fromString("aeee7448-5298-4991-b724-8d5b75a0a7a9");
150 public void tearDown() {
151 AuditEventContextHolder
.clearContext();
155 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#TaxonDaoHibernateImpl()}.
159 public void testInit() {
160 logger
.warn("testInit()");
161 assertNotNull("Instance of ITaxonDao expected",taxonDao
);
162 assertNotNull("Instance of IReferenceDao expected",referenceDao
);
167 * {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getRootTaxa(eu.etaxonomy.cdm.model.reference.Reference)}
172 public void testGetRootTaxa() {
173 Reference sec1
= referenceDao
.findById(1);
174 assert sec1
!= null : "sec1 must exist";
175 Reference sec2
= referenceDao
.findById(2);
176 assert sec2
!= null : "sec2 must exist";
178 List
<Taxon
> rootTaxa
= taxonDao
.getRootTaxa(sec1
);
179 assertNotNull("getRootTaxa should return a List", rootTaxa
);
180 assertFalse("The list should not be empty", rootTaxa
.isEmpty());
181 assertEquals("There should be one root taxon", 1, rootTaxa
.size());
183 rootTaxa
= taxonDao
.getRootTaxa(sec1
, CdmFetch
.FETCH_CHILDTAXA(), true, false);
184 assertNotNull("getRootTaxa should return a List", rootTaxa
);
185 assertFalse("The list should not be empty", rootTaxa
.isEmpty());
186 assertEquals("There should be one root taxon", 1, rootTaxa
.size());
188 rootTaxa
= taxonDao
.getRootTaxa(Rank
.GENUS(), sec1
, CdmFetch
.FETCH_CHILDTAXA(), true, false, null);
189 assertNotNull("getRootTaxa should return a List", rootTaxa
);
190 assertFalse("The list should not be empty", rootTaxa
.isEmpty());
191 assertEquals("There should be one root taxon", 1, rootTaxa
.size());
193 rootTaxa
= taxonDao
.getRootTaxa(Rank
.FAMILY(), sec2
, CdmFetch
.FETCH_CHILDTAXA(), true, false, null);
194 if (logger
.isDebugEnabled()) {
195 logger
.debug("Root taxa rank Family (" + rootTaxa
.size() + "):");
196 for (Taxon taxon
: rootTaxa
) {
197 logger
.debug(taxon
.getTitleCache());
200 assertEquals("There should be one root taxon rank Family", 1, rootTaxa
.size());
201 rootTaxa
= taxonDao
.getRootTaxa(Rank
.GENUS(), sec2
, CdmFetch
.FETCH_CHILDTAXA(), true, false, null);
202 assertNotNull("getRootTaxa should return a List", rootTaxa
);
203 assertFalse("The list should not be empty", rootTaxa
.isEmpty());
204 if (logger
.isDebugEnabled()) {
205 logger
.debug("Root taxa rank Genus (" + rootTaxa
.size() + "):");
206 for (Taxon taxon
: rootTaxa
) {
207 logger
.debug(taxon
.getTitleCache());
210 assertEquals("There should be 22 root taxa rank Genus", 22, rootTaxa
.size());
212 rootTaxa
= taxonDao
.getRootTaxa(Rank
.SPECIES(), sec2
, CdmFetch
.FETCH_CHILDTAXA(), true, false, null);
213 if (logger
.isDebugEnabled()) {
214 logger
.debug("Root taxa rank Species (" + rootTaxa
.size() + "):");
215 for (Taxon taxon
: rootTaxa
) {
216 logger
.debug(taxon
.getTitleCache());
219 assertEquals("There should be 4 root taxa rank Species", 3, rootTaxa
.size());
223 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
227 public void testGetTaxaByName() {
228 Reference
<?
> sec
= referenceDao
.findById(1);
229 assert sec
!= null : "sec must exist";
231 List
<TaxonBase
> results
= taxonDao
.getTaxaByName("Aus", sec
);
232 assertNotNull("getTaxaByName should return a List", results
);
233 //assertFalse("The list should not be empty", results.isEmpty());
234 assertTrue(results
.size() == 1);
236 results
= taxonDao
.getTaxaByName("A*", MatchMode
.BEGINNING
, true, null, null);
237 assertNotNull("getTaxaByName should return a List", results
);
239 int numberOfTaxaByName_A
= 9;
241 logger
.setLevel(Level
.DEBUG
); //FIXME #######################
242 if (logger
.isDebugEnabled()) {
243 for (int i
= 0; i
< results
.size(); i
++) {
244 String nameCache
= "";
245 TaxonNameBase
<?
,?
> taxonNameBase
= ((TaxonBase
)results
.get(i
)).getName();
246 nameCache
= HibernateProxyHelper
.deproxy(taxonNameBase
, NonViralName
.class).getNameCache();
247 logger
.debug(results
.get(i
).getClass() + "(" + i
+")" +
248 ": Name Cache = " + nameCache
+ ", Title Cache = " + results
.get(i
).getTitleCache());
252 assertEquals(numberOfTaxaByName_A
, results
.size());
255 //System.err.println("Species group: " + Rank.SPECIESGROUP().getId() + "Species: " + Rank.SPECIES().getId() + "Section Botany: "+ Rank.SECTION_BOTANY());
257 // assertEquals(results.get(0).getTitleCache(), "Abies sec. ???");
258 // assertEquals(results.get(1).getTitleCache(), "Abies Mill.");
259 // assertEquals(results.get(2).getTitleCache(), "Abies mill. sec. ???");
260 // assertEquals(results.get(3).getTitleCache(), "Abies alba sec. ???");
261 // assertEquals(results.get(4).getTitleCache(), "Abies alba Michx. sec. ???");
262 // assertEquals(results.get(5).getTitleCache(), "Abies alba Mill. sec. ???");
264 results
= taxonDao
.getTaxaByName("A", MatchMode
.BEGINNING
, true, null, null);
265 assertNotNull("getTaxaByName should return a List", results
);
266 assertEquals(numberOfTaxaByName_A
, results
.size());
268 results
= taxonDao
.getTaxaByName("Aus", MatchMode
.EXACT
, true, null, null);
269 assertNotNull("getTaxaByName should return a List", results
);
270 assertEquals("Results list should contain one entity",1,results
.size());
276 @DataSet (loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
277 public void testGetTaxaByNameWithMisappliedNames(){
279 Classification classification
= classificationDao
.load(classificationUuid
);
282 * The testdata contains 3 misapplied names (1. nameCache = Aus, 2. nameCache = Rethera, 3. nameCache = Daphnis), two contained in the classification used in this test,
283 * the other one is not contained in any classification. This latter case is the more general situation.
284 * Misapplied names should be found regardless of whether they are contained in a classification or not.
286 //two accepted taxa starting with R in classification "TestBaum"
287 List
<TaxonBase
> results
= taxonDao
.getTaxaByName(true, false, false, "R*", classification
, MatchMode
.BEGINNING
, null, null, null, null);
288 Assert
.assertEquals("There should be 2 Taxa", 2, results
.size());
290 //three taxa, 2 accepted and 1 misapplied name starting with R
291 results
= taxonDao
.getTaxaByName(true, false, true, "R*", null, MatchMode
.BEGINNING
, null, null, null, null);
292 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
295 results
= taxonDao
.getTaxaByName(true, true, true, "A*", null, MatchMode
.BEGINNING
, null, null, null, null);
296 Assert
.assertEquals("There should be 12 Taxa",12, results
.size());
298 //two accepted taxa in classification and 1 misapplied name with accepted name in classification
299 results
= taxonDao
.getTaxaByName(true, true, true, "R*", classification
, MatchMode
.BEGINNING
, null, null, null, null);
300 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
302 //same as above because all taxa, synonyms and misapplied names starting with R are in the classification
303 results
= taxonDao
.getTaxaByName(true, true, true, "R*", null, MatchMode
.BEGINNING
, null, null, null, null);
304 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
306 //find misapplied names with accepted taxon in the classification, the accepted taxa of two misapplied names are in the classification
307 results
= taxonDao
.getTaxaByName(false, false, true, "*", classification
, MatchMode
.BEGINNING
, null, null, null, null);
308 Assert
.assertEquals("There should be 2 Taxa", 2, results
.size());
310 //find misapplied names beginning with R
311 results
= taxonDao
.getTaxaByName(false, false, true, "R*", null, MatchMode
.BEGINNING
, null, null, null, null);
312 Assert
.assertEquals("There should be 1 Taxa", 1, results
.size());
314 //find all three misapplied names
315 results
= taxonDao
.getTaxaByName(false, false, true, "*", null, MatchMode
.BEGINNING
, null, null, null, null);
316 Assert
.assertEquals("There should be 3 Taxa", 3, results
.size());
321 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}.
325 public void testGetTaxaByNameForEditor() {
326 Reference
<?
> sec
= referenceDao
.findById(1);
327 assert sec
!= null : "sec must exist";
329 List
<UuidAndTitleCache
<TaxonBase
>> results
= taxonDao
.getTaxaByNameForEditor(true, true, "Mand*", null, MatchMode
.BEGINNING
, null);
330 assertNotNull("getTaxaByName should return a List", results
);
331 //assertFalse("The list should not be empty", results.isEmpty());
332 assertTrue(results
.size() == 5);
335 results
= taxonDao
.getTaxaByNameForEditor(true, true,"A*",null, MatchMode
.BEGINNING
, null);
336 assertNotNull("getTaxaByName should return a List", results
);
337 assertTrue(results
.size() == 15);
340 results
= taxonDao
.getTaxaByNameForEditor(true, false,"A", null,MatchMode
.BEGINNING
, null);
341 assertNotNull("getTaxaByName should return a List", results
);
342 assertTrue(results
.size() == 12);
343 assertEquals(results
.get(0).getType(), Taxon
.class);
345 results
= taxonDao
.getTaxaByNameForEditor(false, true,"A", null,MatchMode
.BEGINNING
, null);
346 assertNotNull("getTaxaByName should return a List", results
);
347 assertTrue(results
.size() == 3);
348 assertEquals(results
.get(0).getType(), Synonym
.class);
350 results
= taxonDao
.getTaxaByNameForEditor(true, true,"Aus", null,MatchMode
.EXACT
, null);
351 assertNotNull("getTaxaByName should return a List", results
);
352 assertEquals("Results list should contain one entity",1,results
.size());
357 * Test method for {@link eu.etaxonomy.cdm.persistence.dao.hibernate.taxon.TaxonDaoHibernateImpl#getTaxaByName(java.lang.String, eu.etaxonomy.cdm.model.reference.Reference)}
358 * restricting the search by a set of Areas.
361 @DataSet(loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
362 public void testGetTaxaByNameAndArea() {
364 Set
<NamedArea
> namedAreas
= new HashSet
<NamedArea
>();
365 namedAreas
.add((NamedArea
)definedTermDao
.load(northernAmericaUuid
));
366 //namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
367 //namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
369 Classification taxonmicTree
= classificationDao
.findByUuid(classificationUuid
);
371 // prepare some synonym relation ships for some tests
372 Synonym synAtroposAgassiz
= (Synonym
)taxonDao
.findByUuid(atroposAgassiz
);
373 Taxon taxonRethera
= (Taxon
)taxonDao
.findByUuid(rethera
);
374 taxonRethera
.addSynonym(synAtroposAgassiz
, SynonymRelationshipType
.SYNONYM_OF());
375 logger
.warn("addSynonym(..)");
376 //this.taxonDao.clear();
377 Synonym synAtroposLeach
= (Synonym
)taxonDao
.findByUuid(atroposLeach
);
378 Taxon taxonRetheraSecCdmtest
= (Taxon
)taxonDao
.findByUuid(retheraSecCdmtest
);
379 taxonRetheraSecCdmtest
.addSynonym(synAtroposLeach
, SynonymRelationshipType
.SYNONYM_OF());
380 this.taxonDao
.save(taxonRetheraSecCdmtest
);
381 //this.taxonDao.clear();
382 Taxon test
= (Taxon
)this.taxonDao
.findByUuid(retheraSecCdmtest
);
383 Set
<Synonym
> synonyms
= test
.getSynonyms();
384 // 1. searching for a taxon (Rethera)
385 //long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
387 List
<TaxonBase
> results
= taxonDao
.getTaxaByName(true,false, false, "Rethera", null, MatchMode
.BEGINNING
, namedAreas
,
389 assertNotNull("getTaxaByName should return a List", results
);
390 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 2);
392 // 2. searching for a taxon (Rethera) contained in a specific classification
393 results
= taxonDao
.getTaxaByName(true, false, false, "Rethera", taxonmicTree
, MatchMode
.BEGINNING
, namedAreas
,
395 assertNotNull("getTaxaByName should return a List", results
);
396 assertTrue("expected to find one taxon but found "+results
.size(), results
.size() == 1);
399 // 3. searching for Synonyms
400 results
= taxonDao
.getTaxaByName(false, true, false, "Atropo", null, MatchMode
.ANYWHERE
, null,
402 assertNotNull("getTaxaByName should return a List", results
);
403 /*System.err.println(results.get(0).getTitleCache() + " - " +results.get(1).getTitleCache() + " - " +results.get(2).getTitleCache() );
406 System.err.println(((Synonym)results.get(0)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(1)).getAcceptedTaxa().contains(taxonRethera)+ " - " +((Synonym)results.get(2)).getAcceptedTaxa().contains(taxonRethera)+ " - " );
408 assertTrue("expected to find three taxa but found "+results
.size(), results
.size() == 3);
410 // 4. searching for Synonyms
411 results
= taxonDao
.getTaxaByName(false, true, false, "Atropo", null, MatchMode
.BEGINNING
, null,
413 assertNotNull("getTaxaByName should return a List", results
);
414 assertTrue("expected to find three taxa but found "+results
.size(), results
.size() == 3);
417 // 5. searching for a Synonyms and Taxa
418 // create a synonym relationship first
419 results
= taxonDao
.getTaxaByName(true, true, false, "A", null, MatchMode
.BEGINNING
, namedAreas
,
421 //only five taxa have a distribution
422 assertNotNull("getTaxaByName should return a List", results
);
423 assertTrue("expected to find 7 taxa but found "+results
.size(), results
.size() == 8);
428 * 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)}
429 * restricting the search by a set of Areas.
432 @DataSet(loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
433 public void testFindByNameTitleCache() {
435 Set
<NamedArea
> namedAreas
= new HashSet
<NamedArea
>();
436 namedAreas
.add((NamedArea
)definedTermDao
.load(northernAmericaUuid
));
437 //namedAreas.add((NamedArea)definedTermDao.load(southernAmericaUuid));
438 //namedAreas.add((NamedArea)definedTermDao.load(antarcticaUuid));
440 Classification classification
= classificationDao
.findByUuid(classificationUuid
);
442 // prepare some synonym relation ships for some tests
443 Synonym synAtroposAgassiz
= (Synonym
)taxonDao
.findByUuid(atroposAgassiz
);
444 Taxon taxonRethera
= (Taxon
)taxonDao
.findByUuid(rethera
);
445 taxonRethera
.addSynonym(synAtroposAgassiz
, SynonymRelationshipType
.SYNONYM_OF());
446 logger
.warn("addSynonym(..)");
447 this.taxonDao
.clear();
448 Synonym synAtroposLeach
= (Synonym
)taxonDao
.findByUuid(atroposLeach
);
449 Taxon taxonRetheraSecCdmtest
= (Taxon
)taxonDao
.findByUuid(retheraSecCdmtest
);
450 taxonRetheraSecCdmtest
.addSynonym(synAtroposLeach
, SynonymRelationshipType
.SYNONYM_OF());
451 this.taxonDao
.clear();
452 // 1. searching for a taxon (Rethera)
453 //long numberOfTaxa = taxonDao.countTaxaByName(Taxon.class, "Rethera", null, MatchMode.BEGINNING, namedAreas);
455 List
<TaxonBase
> results
= taxonDao
.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", null, MatchMode
.EXACT
, namedAreas
,
457 assertNotNull("getTaxaByName should return a List", results
);
458 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 2);
460 // 2. searching for a taxon (Rethera) contained in a specific classification
461 results
= taxonDao
.findByNameTitleCache(true, false, "Rethera Rothschild & Jordan, 1903", classification
, MatchMode
.EXACT
, namedAreas
,
463 assertNotNull("getTaxaByName should return a List", results
);
464 assertTrue("expected to find one taxon but found "+results
.size(), results
.size() == 1);
467 // 3. searching for Synonyms
468 results
= taxonDao
.findByNameTitleCache(false, true, "Atropo", null, MatchMode
.ANYWHERE
, null,
470 assertNotNull("getTaxaByName should return a List", results
);
472 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 3);
474 // 4. searching for Synonyms
475 results
= taxonDao
.findByNameTitleCache(false, true, "Atropo", null, MatchMode
.BEGINNING
, null,
477 assertNotNull("getTaxaByName should return a List", results
);
478 assertTrue("expected to find two taxa but found "+results
.size(), results
.size() == 3);
481 // 5. searching for a Synonyms and Taxa
482 // create a synonym relationship first
483 results
= taxonDao
.findByNameTitleCache(true, true, "A", null, MatchMode
.BEGINNING
, namedAreas
,
485 assertNotNull("getTaxaByName should return a List", results
);
486 assertTrue("expected to find 8 taxa but found "+results
.size(), results
.size() == 8);
490 @DataSet(loadStrategy
=CleanSweepInsertLoadStrategy
.class, value
="TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
491 public void testTaxonNameInTwoClassifications(){
492 int numberOfClassifications
= classificationDao
.count();
493 List
<String
> propertyPaths
= new ArrayList
<String
>();
494 propertyPaths
.add("taxonNodes");
495 List
<TaxonBase
> taxa
= taxonDao
.getTaxaByName(true, true, false, "P*", null, MatchMode
.BEGINNING
, null, null, null, null);
496 Taxon taxon
= (Taxon
)taxa
.get(0);
497 Set
<TaxonNode
> nodes
= taxon
.getTaxonNodes();
498 assertTrue(nodes
.size() == 1);
499 //assertNotNull(taxa);
500 //assertTrue(taxa.size() > 0);
505 public void testFindByUuid() {
506 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(uuid
);
507 assertNotNull("findByUuid should return a taxon",taxon
);
508 assertFalse("findByUuid should not return a taxon with it's name initialized",Hibernate
.isInitialized(taxon
.getName()));
513 public void testLoad() {
514 List
<String
> propertyPaths
= new ArrayList
<String
>();
515 propertyPaths
.add("name");
516 propertyPaths
.add("sec");
517 Taxon taxon
= (Taxon
)taxonDao
.load(uuid
, propertyPaths
);
518 assertNotNull("findByUuid should return a taxon",taxon
);
519 assertTrue("load should return a taxon with it's name initialized, given that the property was specified in the method",Hibernate
.isInitialized(taxon
.getName()));
520 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()));
525 public void testCountTaxonRelationships() {
526 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
527 assert taxon
!= null : "taxon must exist";
529 int numberOfRelatedTaxa
= taxonDao
.countTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship
.Direction
.relatedTo
);
530 assertEquals("countTaxonRelationships should return 23", 23, numberOfRelatedTaxa
);
535 public void testCountTaxaByName() {
536 long numberOfTaxa
= taxonDao
.countTaxaByName(true, false, false, "A*", null, MatchMode
.BEGINNING
, null);
537 assertEquals(numberOfTaxa
, 12);
538 numberOfTaxa
= taxonDao
.countTaxaByName(true, false, false, "A*", null, MatchMode
.BEGINNING
, null);
539 assertEquals(numberOfTaxa
, 12);
540 numberOfTaxa
= taxonDao
.countTaxaByName(false, true, false, "A*", null, MatchMode
.BEGINNING
, null);
541 assertEquals(numberOfTaxa
, 3);
542 numberOfTaxa
= taxonDao
.countTaxaByName(true, true, false, "A*", null, MatchMode
.BEGINNING
, null);
543 assertEquals(numberOfTaxa
, 15);
544 numberOfTaxa
= taxonDao
.countTaxaByName(true, true, false, "Aasfwerfwf fffe", null, MatchMode
.BEGINNING
, null);
545 assertEquals(numberOfTaxa
, 0);
546 // FIXME implement test for search in specific classification
547 // Reference reference = referenceDao.findByUuid(UUID.fromString("596b1325-be50-4b0a-9aa2-3ecd610215f2"));
548 // numberOfTaxa = taxonDao.countTaxaByName("A*", MatchMode.BEGINNING, SelectMode.ALL, null, null);
549 // assertEquals(numberOfTaxa, 2);
554 public void testRelatedTaxa() {
555 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
556 assert taxon
!= null : "taxon must exist";
558 List
<String
> propertyPaths
= new ArrayList
<String
>();
559 propertyPaths
.add("fromTaxon");
560 propertyPaths
.add("fromTaxon.name");
561 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
562 orderHints
.add(new OrderHint("relatedFrom.name.genusOrUninomial", SortOrder
.ASCENDING
));
563 orderHints
.add(new OrderHint("relatedFrom.name.specificEpithet", SortOrder
.ASCENDING
));
564 orderHints
.add(new OrderHint("relatedFrom.name.infraSpecificEpithet", SortOrder
.ASCENDING
));
566 List
<TaxonRelationship
> relatedTaxa
= taxonDao
.getTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), null, null, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
567 assertNotNull("getRelatedTaxa should return a List",relatedTaxa
);
568 assertEquals("getRelatedTaxa should return all 23 related taxa",relatedTaxa
.size(),23);
569 assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate
.isInitialized(relatedTaxa
.get(0).getFromTaxon()));
570 assertTrue("getRelatedTaxa should return TaxonRelationship objects with the relatedFrom taxon initialized",Hibernate
.isInitialized(relatedTaxa
.get(0).getFromTaxon().getName()));
572 assertEquals("Acherontia should appear first in the list of related taxa", relatedTaxa
.get(0).getFromTaxon().getTitleCache(), "Acherontia Laspeyres, 1809 sec. cate-sphingidae.org");
573 assertEquals("Sphingonaepiopsis should appear last in the list of related taxa", relatedTaxa
.get(22).getFromTaxon().getTitleCache(), "Sphinx Linnaeus, 1758 sec. cate-sphingidae.org");
578 public void testGetRelatedTaxaPaged() {
579 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
580 assert taxon
!= null : "taxon must exist";
582 List
<String
> propertyPaths
= new ArrayList
<String
>();
583 propertyPaths
.add("fromTaxon");
584 propertyPaths
.add("fromTaxon.name");
586 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
587 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
589 List
<TaxonRelationship
> firstPage
= taxonDao
.getTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), 10, 0, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
590 List
<TaxonRelationship
> secondPage
= taxonDao
.getTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(),10, 1, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
591 List
<TaxonRelationship
> thirdPage
= taxonDao
.getTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), 10, 2, orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedTo
);
593 assertNotNull("getRelatedTaxa: 10, 0 should return a List",firstPage
);
594 assertEquals("getRelatedTaxa: 10, 0 should return a List with 10 elements",10,firstPage
.size());
595 assertNotNull("getRelatedTaxa: 10, 1 should return a List",secondPage
);
596 assertEquals("getRelatedTaxa: 10, 1 should return a List with 10 elements",secondPage
.size(),10);
597 assertNotNull("getRelatedTaxa: 10, 2 should return a List",thirdPage
);
598 assertEquals("getRelatedTaxa: 10, 2 should return a List with 3 elements",thirdPage
.size(),3);
603 public void testCountSynonymRelationships() {
604 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
605 assert taxon
!= null : "taxon must exist";
607 int numberOfSynonymRelationships
= taxonDao
.countSynonyms(taxon
,null);
608 assertEquals("countSynonymRelationships should return 5",5,numberOfSynonymRelationships
);
613 public void testSynonymRelationships() {
614 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
615 assert taxon
!= null : "taxon must exist";
616 List
<String
> propertyPaths
= new ArrayList
<String
>();
617 propertyPaths
.add("synonym");
618 propertyPaths
.add("synonym.name");
620 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
621 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
623 List
<SynonymRelationship
> synonyms
= taxonDao
.getSynonyms(taxon
, null, null, null,orderHints
,propertyPaths
);
625 assertNotNull("getSynonyms should return a List",synonyms
);
626 assertEquals("getSynonyms should return 5 SynonymRelationship entities",synonyms
.size(),5);
627 assertTrue("getSynonyms should return SynonymRelationship objects with the synonym initialized",Hibernate
.isInitialized(synonyms
.get(0).getSynonym()));
632 public void testCountSynonymRelationshipsByType() {
633 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
634 assert taxon
!= null : "taxon must exist";
636 int numberOfTaxonomicSynonyms
= taxonDao
.countSynonyms(taxon
, SynonymRelationshipType
.HETEROTYPIC_SYNONYM_OF());
637 assertEquals("countSynonyms should return 4",numberOfTaxonomicSynonyms
, 4);
642 public void testSynonymRelationshipsByType() {
643 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
644 assert taxon
!= null : "taxon must exist";
646 List
<SynonymRelationship
> synonyms
= taxonDao
.getSynonyms(taxon
, SynonymRelationshipType
.HETEROTYPIC_SYNONYM_OF(), null, null,null,null);
648 assertNotNull("getSynonyms should return a List",synonyms
);
649 assertEquals("getSynonyms should return 4 SynonymRelationship entities",synonyms
.size(),4);
654 public void testPageSynonymRelationships(){
655 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
656 assert taxon
!= null : "taxon must exist";
658 List
<SynonymRelationship
> firstPage
= taxonDao
.getSynonyms(taxon
, null, 4, 0,null,null);
659 List
<SynonymRelationship
> secondPage
= taxonDao
.getSynonyms(taxon
, null, 4, 1,null,null);
661 assertNotNull("getSynonyms: 4, 0 should return a List",firstPage
);
662 assertEquals("getSynonyms: 4, 0 should return 4 SynonymRelationships", firstPage
.size(),4);
663 assertNotNull("getSynonyms: 4, 1 should return a List",secondPage
);
664 assertEquals("getSynonyms: 4, 1 should return 1 SynonymRelationship",secondPage
.size(),1);
669 public void testGetTaxonMatchingUninomial() {
670 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class, "Smerinthus", "*", "*", "*",null,null,null);
672 assertNotNull("findTaxaByName should return a List", result
);
673 assertEquals("findTaxaByName should return two Taxa",2,result
.size());
674 assertEquals("findTaxaByName should return a Taxon with id 5",5,result
.get(0).getId());
679 public void testGetTaxonMatchingSpeciesBinomial() {
680 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class,"Smerinthus", null, "kindermannii", null,null,null,null);
682 assertNotNull("findTaxaByName should return a List", result
);
683 assertEquals("findTaxaByName should return one Taxon",1,result
.size());
684 assertEquals("findTaxaByName should return a Taxon with id 8",8,result
.get(0).getId());
689 public void testGetTaxonMatchingTrinomial() {
690 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class,"Cryptocoryne", null,"purpurea","borneoensis",null,null,null);
692 assertNotNull("findTaxaByName should return a List", result
);
693 assertEquals("findTaxaByName should return one Taxon",1,result
.size());
694 assertEquals("findTaxaByName should return a Taxon with id 38",38,result
.get(0).getId());
699 public void testNegativeMatch() {
700 List
<TaxonBase
> result
= taxonDao
.findTaxaByName(Taxon
.class,"Acherontia", null,"atropos","dehli",null,null,null);
702 assertNotNull("findTaxaByName should return a List", result
);
703 assertTrue("findTaxaByName should return an empty List",result
.isEmpty());
708 public void testCountAllTaxa() {
709 int numberOfTaxa
= taxonDao
.count(Taxon
.class);
710 assertEquals("count should return 36 taxa",36, numberOfTaxa
);
715 public void testListAllTaxa() {
716 List
<TaxonBase
> taxa
= taxonDao
.list(Taxon
.class,100, 0);
717 assertNotNull("list should return a List",taxa
);
718 assertEquals("list should return 36 taxa",36, taxa
.size());
724 public void testDelete() {
725 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
726 assert taxon
!= null : "taxon must exist";
727 taxonDao
.delete(taxon
);
731 printDataSet(new FileOutputStream("test.xml"), TABLE_NAMES
);
732 } catch (FileNotFoundException e
) {
739 public void testDeleteWithChildren() {
740 Taxon taxonWithChildren
= (Taxon
)taxonDao
.findByUuid(mimas
);
741 assert taxonWithChildren
!= null : "taxon must exist";
742 assertEquals(taxonWithChildren
.getTaxonomicChildrenCount(), 2);
743 Taxon parent
= (Taxon
)taxonDao
.findByUuid(sphingidae
);
744 assertSame(taxonWithChildren
.getTaxonomicParent(), parent
);
745 assertEquals(parent
.getTaxonomicChildrenCount(), 204);
746 taxonDao
.delete(taxonWithChildren
);
747 assertEquals(parent
.getTaxonomicChildrenCount(), 203);
751 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
752 public void testFindDeleted() {
753 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(acherontia
);
754 assertNull("findByUuid should return null in this view", taxon
);
755 assertFalse("exist should return false in this view",taxonDao
.exists(acherontia
));
759 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
760 public void testFindDeletedInPreviousView() {
761 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
762 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontia
);
763 assertNotNull("findByUuid should return a taxon in this view",taxon
);
764 assertTrue("exists should return true in this view", taxonDao
.exists(acherontia
));
767 assertEquals("There should be 3 relations to this taxon in this view",3,taxon
.getRelationsToThisTaxon().size());
768 } catch(Exception e
) {
769 fail("We should not experience any problems initializing proxies with envers");
774 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
775 public void testGetAuditEvents() {
776 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
777 assert taxon
!= null : "taxon cannot be null";
779 List
<String
> propertyPaths
= new ArrayList
<String
>();
780 propertyPaths
.add("name");
781 propertyPaths
.add("createdBy");
782 propertyPaths
.add("updatedBy");
784 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(taxon
, null,null,null,propertyPaths
);
785 assertNotNull("getAuditEvents should return a list",auditEvents
);
786 assertFalse("the list should not be empty",auditEvents
.isEmpty());
787 assertEquals("There should be two AuditEventRecords in the list",2, auditEvents
.size());
791 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
792 public void testGetAuditEventsFromNow() {
793 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
794 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
795 assert taxon
!= null : "taxon cannot be null";
797 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(taxon
, null,null,AuditEventSort
.FORWARDS
,null);
798 assertNotNull("getAuditEvents should return a list",auditEvents
);
799 assertFalse("the list should not be empty",auditEvents
.isEmpty());
800 assertEquals("There should be one audit event in the list",1,auditEvents
.size());
804 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
805 public void testCountAuditEvents() {
806 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
807 assert taxon
!= null : "taxon cannot be null";
809 int numberOfAuditEvents
= taxonDao
.countAuditEvents(taxon
,null);
810 assertEquals("countAuditEvents should return 2",numberOfAuditEvents
,2);
814 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
815 public void getPreviousAuditEvent() {
816 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
817 assert taxon
!= null : "taxon cannot be null";
819 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getPreviousAuditEvent(taxon
);
820 assertNotNull("getPreviousAuditEvent should not return null as there is at least one audit event prior to the current one",auditEvent
);
824 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
825 public void getPreviousAuditEventAtBeginning() {
826 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
827 TaxonBase taxon
= taxonDao
.findByUuid(sphingidae
);
828 assert taxon
!= null : "taxon cannot be null";
830 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getPreviousAuditEvent(taxon
);
831 assertNull("getPreviousAuditEvent should return null if we're at the first audit event anyway",auditEvent
);
835 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
836 public void getNextAuditEvent() {
837 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
838 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
839 assert taxon
!= null : "taxon cannot be null";
841 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getNextAuditEvent(taxon
);
842 assertNotNull("getNextAuditEvent should not return null as there is at least one audit event after the current one",auditEvent
);
846 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
847 public void getNextAuditEventAtEnd() {
848 AuditEventContextHolder
.getContext().setAuditEvent(mostRecentAuditEvent
);
849 TaxonBase
<?
> taxon
= taxonDao
.findByUuid(sphingidae
);
850 assert taxon
!= null : "taxon cannot be null";
852 AuditEventRecord
<TaxonBase
> auditEvent
= taxonDao
.getNextAuditEvent(taxon
);
853 assertNull("getNextAuditEvent should return null as there no more audit events after the current one",auditEvent
);
860 public void testAddChild() throws Exception
{
861 Taxon parent
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
862 assert parent
!= null : "taxon cannot be null";
863 Taxon child
= Taxon
.NewInstance(null, null);
864 child
.setTitleCache("Acherontia lachesis diehli Eitschberger, 2003", true);
865 child
.addTaxonRelation(parent
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(),null, null);
866 taxonDao
.save(child
);
872 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
873 public void testFind() {
874 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
875 assert taxon
!= null : "taxon cannot be null";
877 assertEquals("getTaxonomicChildrenCount should return 1 in this view",1,taxon
.getTaxonomicChildrenCount());
878 assertEquals("getRelationsToThisTaxon should contain 1 TaxonRelationship in this view",1,taxon
.getRelationsToThisTaxon().size());
882 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
883 public void testFindInPreviousView() {
884 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
885 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
886 assert taxon
!= null : "taxon cannot be null";
888 assertEquals("getTaxonomicChildrenCount should return 0 in this view",0,taxon
.getTaxonomicChildrenCount());
889 assertTrue("getRelationsToThisTaxon should contain 0 TaxonRelationship in this view",taxon
.getRelationsToThisTaxon().isEmpty());
893 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
894 public void testGetRelations() {
895 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
896 assert taxon
!= null : "taxon cannot be null";
898 List
<String
> propertyPaths
= new ArrayList
<String
>();
899 propertyPaths
.add("fromTaxon");
900 propertyPaths
.add("fromTaxon.name");
902 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
903 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
905 List
<TaxonRelationship
> taxonRelations
= taxonDao
.getTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedFrom
);
906 assertNotNull("getRelatedTaxa should return a list", taxonRelations
);
907 assertEquals("there should be one TaxonRelationship in the list in the current view",1,taxonRelations
.size());
908 assertTrue("TaxonRelationship.relatedFrom should be initialized",Hibernate
.isInitialized(taxonRelations
.get(0).getFromTaxon()));
909 assertTrue("TaxonRelationship.relatedFrom.name should be initialized",Hibernate
.isInitialized(taxonRelations
.get(0).getFromTaxon().getName()));
913 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
914 public void testCountRelations() {
915 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
916 assert taxon
!= null : "taxon cannot be null";
917 assertEquals("countRelatedTaxa should return 1 in the current view",1, taxonDao
.countTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship
.Direction
.relatedTo
));
921 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
922 public void testGetRelationsInPreviousView() {
923 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
924 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
925 assert taxon
!= null : "taxon cannot be null";
927 List
<String
> propertyPaths
= new ArrayList
<String
>();
928 propertyPaths
.add("relatedFrom");
929 propertyPaths
.add("relatedFrom.name");
931 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
932 orderHints
.add(new OrderHint("relatedFrom.titleCache", SortOrder
.ASCENDING
));
934 List
<TaxonRelationship
> taxonRelations
= taxonDao
.getTaxonRelationships(taxon
, TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), null, null,orderHints
,propertyPaths
, TaxonRelationship
.Direction
.relatedFrom
);
935 assertNotNull("getRelatedTaxa should return a list",taxonRelations
);
936 assertTrue("there should be no TaxonRelationships in the list in the prior view",taxonRelations
.isEmpty());
940 @DataSet("TaxonDaoHibernateImplTest.testFind.xml")
941 public void testCountRelationsInPreviousView() {
942 AuditEventContextHolder
.getContext().setAuditEvent(previousAuditEvent
);
943 Taxon taxon
= (Taxon
)taxonDao
.findByUuid(acherontiaLachesis
);
944 assert taxon
!= null : "taxon cannot be null";
945 assertEquals("countRelatedTaxa should return 0 in the current view",0, taxonDao
.countTaxonRelationships(taxon
,TaxonRelationshipType
.TAXONOMICALLY_INCLUDED_IN(), TaxonRelationship
.Direction
.relatedTo
));
950 public void testGroupTaxa() {
951 List
<Grouping
> groups
= new ArrayList
<Grouping
>();
952 groups
.add(new GroupByCount("count",SortOrder
.DESCENDING
));
953 groups
.add(new Grouping("name.genusOrUninomial", "genus", "n", SortOrder
.ASCENDING
));
954 List
<Object
[]> results
= taxonDao
.group(null, null, null, groups
,null);
955 System
.out
.println("count\tname.genuOrUninomial");
956 for(Object
[] result
: results
) {
957 System
.out
.println(result
[0] + "\t" + result
[1]);
963 public void testGroupTaxaByClass() {
964 List
<Grouping
> groups
= new ArrayList
<Grouping
>();
965 groups
.add(new GroupByCount("count",SortOrder
.DESCENDING
));
966 groups
.add(new Grouping("class", "class",null, SortOrder
.ASCENDING
));
967 List
<Object
[]> results
= taxonDao
.group(null, null, null, groups
,null);
968 System
.out
.println("count\tclass");
969 for(Object
[] result
: results
) {
970 System
.out
.println(result
[0] + "\t" + result
[1]);
976 public void testNativeSQLOrder() {
977 List
<OrderHint
> orderHints
= new ArrayList
<OrderHint
>();
978 orderHints
.add(new NativeSqlOrderHint("case when {alias}.titleCache like 'C%' then 0 else 1 end",SortOrder
.ASCENDING
));
980 List
<TaxonBase
> results
= taxonDao
.list(null, null, orderHints
);
981 System
.out
.println("native SQL order");
982 for(TaxonBase
<?
> result
: results
) {
983 System
.out
.println(result
.getTitleCache());
989 public void testGroupByDateTaxa() {
990 List
<Grouping
> groups
= new ArrayList
<Grouping
>();
991 groups
.add(new GroupByCount("count",null));
992 groups
.add(new GroupByDate("created", "dateGroup", SortOrder
.ASCENDING
, GroupByDate
.Resolution
.MONTH
));
993 List
<Object
[]> results
= taxonDao
.group(null, null, null, groups
,null);
994 System
.out
.println("count\tyear\tmonth");
995 for(Object
[] result
: results
) {
996 System
.out
.println(result
[0] + "\t" + result
[1] + "\t" + result
[2]);
1001 @DataSet ("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
1002 public final void testGetTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(){
1003 Classification classification
= classificationDao
.findByUuid(classificationUuid
);
1004 assertNotNull(taxonDao
.getTaxonNodeUuidAndTitleCacheOfAcceptedTaxaByClassification(classification
));
1008 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
1009 public void testGetAuditEventsByType() {
1011 List
<String
> propertyPaths
= new ArrayList
<String
>();
1012 propertyPaths
.add("name");
1013 propertyPaths
.add("createdBy");
1014 propertyPaths
.add("updatedBy");
1016 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(TaxonBase
.class, previousAuditEvent
, mostRecentAuditEvent
, null,null, null, AuditEventSort
.FORWARDS
, propertyPaths
);
1017 assertNotNull("getAuditEvents should return a list",auditEvents
);
1018 assertFalse("the list should not be empty",auditEvents
.isEmpty());
1019 assertEquals("There should be thirty eight AuditEventRecords in the list",38, auditEvents
.size());
1024 @DataSet("TaxonDaoHibernateImplTest.testFindDeleted.xml")
1025 public void testGetAuditEventsByTypeWithRestrictions() {
1027 List
<String
> propertyPaths
= new ArrayList
<String
>();
1028 propertyPaths
.add("name");
1029 propertyPaths
.add("createdBy");
1030 propertyPaths
.add("updatedBy");
1032 List
<AuditCriterion
> criteria
= new ArrayList
<AuditCriterion
>();
1033 criteria
.add(AuditEntity
.property("lsid_lsid").isNotNull());
1035 List
<AuditEventRecord
<TaxonBase
>> auditEvents
= taxonDao
.getAuditEvents(TaxonBase
.class, previousAuditEvent
, mostRecentAuditEvent
, criteria
,null, null, AuditEventSort
.FORWARDS
, propertyPaths
);
1036 assertNotNull("getAuditEvents should return a list",auditEvents
);
1037 assertFalse("the list should not be empty",auditEvents
.isEmpty());
1038 assertEquals("There should be one AuditEventRecord in the list",1, auditEvents
.size());
1041 @DataSet("TaxonDaoHibernateImplTest.testGetTaxaByNameAndArea.xml")
1042 public void testGetCommonName(){
1045 List
<Object
[]> commonNameResults
= taxonDao
.getTaxaByCommonName("common%", null,
1046 MatchMode
.BEGINNING
, null, null, null, null);
1048 assertNotNull("getTaxaByCommonName should return a list", commonNameResults
);
1049 assertFalse("the list should not be empty", commonNameResults
.isEmpty());
1050 assertEquals("There should be one Taxon with common name", 1,commonNameResults
.size());
1051 assertEquals(" sec. ???", ((TaxonBase
)commonNameResults
.get(0)[0]).getTitleCache());
1057 // public void testDeploy(){
1058 // TaxonBase taxonBase = taxonDao.findByUuid(UUID.fromString("6bfedf25-6dbc-4d5c-9d56-84f9052f3b2a"));
1060 // Synonym synonym = taxonBase.deproxy(taxonBase, Synonym.class);