|
1
|
/**
|
|
2
|
* Copyright (C) 2009 EDIT
|
|
3
|
* European Distributed Institute of Taxonomy
|
|
4
|
* http://www.e-taxonomy.eu
|
|
5
|
*
|
|
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.
|
|
8
|
*/
|
|
9
|
|
|
10
|
package eu.etaxonomy.cdm.api.service;
|
|
11
|
|
|
12
|
import java.io.FileNotFoundException;
|
|
13
|
import java.util.UUID;
|
|
14
|
|
|
15
|
import org.apache.log4j.Logger;
|
|
16
|
import org.junit.Assert;
|
|
17
|
import org.junit.Test;
|
|
18
|
import org.unitils.database.annotations.Transactional;
|
|
19
|
import org.unitils.database.util.TransactionMode;
|
|
20
|
import org.unitils.dbunit.annotation.DataSet;
|
|
21
|
import org.unitils.dbunit.annotation.ExpectedDataSet;
|
|
22
|
import org.unitils.spring.annotation.SpringBeanByType;
|
|
23
|
|
|
24
|
import eu.etaxonomy.cdm.api.service.dto.IdentifiedEntityDTO;
|
|
25
|
import eu.etaxonomy.cdm.api.service.dto.MarkedEntityDTO;
|
|
26
|
import eu.etaxonomy.cdm.api.service.pager.Pager;
|
|
27
|
import eu.etaxonomy.cdm.model.common.CdmBase;
|
|
28
|
import eu.etaxonomy.cdm.model.common.DefinedTerm;
|
|
29
|
import eu.etaxonomy.cdm.model.common.Identifier;
|
|
30
|
import eu.etaxonomy.cdm.model.common.MarkerType;
|
|
31
|
import eu.etaxonomy.cdm.model.common.TermVocabulary;
|
|
32
|
import eu.etaxonomy.cdm.model.common.VocabularyEnum;
|
|
33
|
import eu.etaxonomy.cdm.model.name.IBotanicalName;
|
|
34
|
import eu.etaxonomy.cdm.model.name.Rank;
|
|
35
|
import eu.etaxonomy.cdm.model.name.TaxonName;
|
|
36
|
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
|
|
37
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
|
38
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
|
39
|
import eu.etaxonomy.cdm.model.taxon.SynonymType;
|
|
40
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
|
41
|
import eu.etaxonomy.cdm.model.taxon.TaxonBase;
|
|
42
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
|
43
|
import eu.etaxonomy.cdm.persistence.query.MatchMode;
|
|
44
|
import eu.etaxonomy.cdm.persistence.query.TaxonTitleType;
|
|
45
|
import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
|
|
46
|
|
|
47
|
/**
|
|
48
|
* @author a.mueller
|
|
49
|
*
|
|
50
|
*/
|
|
51
|
@Transactional(TransactionMode.DISABLED)
|
|
52
|
public class IdentifiableServiceBaseTest extends CdmTransactionalIntegrationTest {
|
|
53
|
@SuppressWarnings("unused")
|
|
54
|
private static final Logger logger = Logger.getLogger(IdentifiableServiceBaseTest.class);
|
|
55
|
|
|
56
|
|
|
57
|
@SpringBeanByType
|
|
58
|
private INameService nameService;
|
|
59
|
|
|
60
|
@SpringBeanByType
|
|
61
|
private ITermService termService;
|
|
62
|
|
|
63
|
@SpringBeanByType
|
|
64
|
private IVocabularyService vocService;
|
|
65
|
|
|
66
|
@SpringBeanByType
|
|
67
|
private ITaxonService taxonService;
|
|
68
|
|
|
69
|
@SpringBeanByType
|
|
70
|
private IClassificationService classificationService;
|
|
71
|
|
|
72
|
/****************** TESTS *****************************/
|
|
73
|
|
|
74
|
@Test
|
|
75
|
public final void voidTestSeriveExists(){
|
|
76
|
Assert.assertNotNull("Service shoulb be initialized", nameService);
|
|
77
|
}
|
|
78
|
|
|
79
|
|
|
80
|
@Test
|
|
81
|
@DataSet
|
|
82
|
@ExpectedDataSet
|
|
83
|
public final void testUpdateTitleCache() {
|
|
84
|
Assert.assertEquals("There should be 5 TaxonNames in the data set", 5, nameService.count(TaxonName.class));
|
|
85
|
Class clazz = TaxonName.class;
|
|
86
|
int stepSize = 2;
|
|
87
|
nameService.updateTitleCache(clazz, stepSize, null, null);
|
|
88
|
commit();
|
|
89
|
// commitAndStartNewTransaction(new String[]{"TaxonName","TaxonName_AUD"});
|
|
90
|
}
|
|
91
|
|
|
92
|
|
|
93
|
@Test
|
|
94
|
@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
|
|
95
|
public final void testFindByIdentifier(){
|
|
96
|
UUID uuidIdentifierType1 = UUID.fromString("02bb62db-a229-4eeb-83e6-a9a093943d5e");
|
|
97
|
UUID uuidIdentifierType2 = UUID.fromString("ef6e960f-5289-456c-b25c-cff7f4de2f63");
|
|
98
|
|
|
99
|
|
|
100
|
DefinedTerm it1 = (DefinedTerm)termService.find(uuidIdentifierType1);
|
|
101
|
Assert.assertNotNull("identifier type must not be null", it1);
|
|
102
|
|
|
103
|
boolean includeEntity = true;
|
|
104
|
Pager<IdentifiedEntityDTO<Taxon>> taxonPager = taxonService.findByIdentifier(Taxon.class, "ext-1234", it1, null, includeEntity, null, null, null);
|
|
105
|
Assert.assertTrue("Result should not be empty", taxonPager.getCount() == 1);
|
|
106
|
IdentifiedEntityDTO<Taxon>.CdmEntity entity = taxonPager.getRecords().get(0).getCdmEntity();
|
|
107
|
Taxon taxon = entity.getEntity();
|
|
108
|
Assert.assertEquals(UUID.fromString("888cded1-cadc-48de-8629-e32927919879"), taxon.getUuid());
|
|
109
|
Assert.assertEquals(UUID.fromString("888cded1-cadc-48de-8629-e32927919879"), entity.getCdmUuid());
|
|
110
|
Assert.assertEquals("Taxon should have 1 identifier", 1, taxon.getIdentifiers().size());
|
|
111
|
Identifier<?> identifier = taxon.getIdentifiers().get(0);
|
|
112
|
DefinedTerm type = CdmBase.deproxy(identifier.getType(), DefinedTerm.class);
|
|
113
|
Assert.assertEquals(uuidIdentifierType1, type.getUuid());
|
|
114
|
|
|
115
|
Pager<IdentifiedEntityDTO<TaxonName>> names = nameService.findByIdentifier(
|
|
116
|
TaxonName.class, "ext-1234", null, null, includeEntity, null, null, null);
|
|
117
|
Assert.assertTrue("Identifier does not exist for TaxonName", names.getCount() == 0);
|
|
118
|
|
|
119
|
taxonPager = taxonService.findByIdentifier(null, "ext-1234", null, null, includeEntity, null, null, null);
|
|
120
|
Assert.assertEquals("Result size for 'ext-1234' should be 1", 1, taxonPager.getRecords().size());
|
|
121
|
|
|
122
|
taxonPager = taxonService.findByIdentifier(Taxon.class, null, null, null, includeEntity, null, null, null);
|
|
123
|
Assert.assertEquals("Result should not be empty", 2 , taxonPager.getRecords().size());
|
|
124
|
|
|
125
|
//includeEntity
|
|
126
|
includeEntity = false;
|
|
127
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "ext-1234", it1, null, includeEntity, null, null, null);
|
|
128
|
entity = taxonPager.getRecords().get(0).getCdmEntity();
|
|
129
|
Assert.assertNull("Taxon must not be returned with includeEntity = false", entity.getEntity());
|
|
130
|
|
|
131
|
|
|
132
|
|
|
133
|
//Matchmode
|
|
134
|
includeEntity = false;
|
|
135
|
MatchMode matchmode = null;
|
|
136
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, matchmode, includeEntity, null, null, null);
|
|
137
|
Assert.assertTrue("Result size for '123' should be 0", taxonPager.getCount() == 0);
|
|
138
|
|
|
139
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, MatchMode.EXACT, includeEntity, null, null, null);
|
|
140
|
Assert.assertTrue("Result size for '123' should be 0", taxonPager.getCount() == 0);
|
|
141
|
|
|
142
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, MatchMode.ANYWHERE, includeEntity, null, null, null);
|
|
143
|
Assert.assertTrue("Result size for '123' should be 1", taxonPager.getCount() == 1);
|
|
144
|
|
|
145
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "123", null, MatchMode.BEGINNING, includeEntity, null, null, null);
|
|
146
|
Assert.assertTrue("Result size for '123' should be 0", taxonPager.getCount() == 0);
|
|
147
|
|
|
148
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "ext", null, MatchMode.BEGINNING, includeEntity, null, null, null);
|
|
149
|
Assert.assertTrue("Result size for 'ext' should be 1", taxonPager.getCount() == 2);
|
|
150
|
|
|
151
|
//Paging
|
|
152
|
taxonPager = taxonService.findByIdentifier(null, "ext", null, MatchMode.BEGINNING, includeEntity, null, null, null);
|
|
153
|
Assert.assertEquals("Total result size for starts with 'ext' should be 4", 4, taxonPager.getRecords().size());
|
|
154
|
taxonPager = taxonService.findByIdentifier(null, "ext", null, MatchMode.BEGINNING, includeEntity, 2, 1, null);
|
|
155
|
Assert.assertEquals("Total result size for starts with 'ext' should be 4", Long.valueOf(4), taxonPager.getCount());
|
|
156
|
Assert.assertEquals("Result size for starts with 'ext' second page should be 2", Integer.valueOf(2), taxonPager.getPageSize());
|
|
157
|
Assert.assertEquals("The third taxon (first on second page) should be ext-syn1", "ext-syn1", taxonPager.getRecords().get(0).getIdentifier().getIdentifier());
|
|
158
|
|
|
159
|
taxonPager = taxonService.findByIdentifier(Taxon.class, "ext", null, MatchMode.BEGINNING, includeEntity, null, null, null);
|
|
160
|
Assert.assertTrue("Result size for 'ext' should be 2", taxonPager.getCount() == 2);
|
|
161
|
|
|
162
|
}
|
|
163
|
|
|
164
|
@Test
|
|
165
|
@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
|
|
166
|
public final void testFindByIdentifierClassification(){
|
|
167
|
//classification Filter
|
|
168
|
Classification classification = classificationService.find(5000);
|
|
169
|
TaxonNode rootNode = classification.getRootNode();
|
|
170
|
Pager<IdentifiedEntityDTO<Taxon>> taxonPager = taxonService.findByIdentifier(Taxon.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null, null);
|
|
171
|
Assert.assertEquals("Result size for 'ext' should be 1", Long.valueOf(1), taxonPager.getCount());
|
|
172
|
Assert.assertEquals("Result size for 'ext' should be 1", 1, taxonPager.getRecords().size());
|
|
173
|
|
|
174
|
Pager<IdentifiedEntityDTO<Taxon>> taxPager = taxonService.findByIdentifier(Taxon.class, "ext-cache1", null, rootNode, MatchMode.EXACT, false, null, null, null);
|
|
175
|
Assert.assertEquals("Result size for 'ext' should be 0", Long.valueOf(0), taxPager.getCount());
|
|
176
|
Assert.assertEquals("Result size for 'ext' should be 0", 0, taxPager.getRecords().size());
|
|
177
|
|
|
178
|
rootNode = null; //check against missing filter
|
|
179
|
taxPager = taxonService.findByIdentifier(Taxon.class, "ext-cache1", null, rootNode, MatchMode.EXACT, false, null, null, null);
|
|
180
|
Assert.assertEquals("Result size for 'ext-cache1' without filter should be 1", Long.valueOf(1), taxPager.getCount());
|
|
181
|
Assert.assertEquals("Result size for 'ext-cache1' without filter should be 1", 1, taxPager.getRecords().size());
|
|
182
|
|
|
183
|
//TaxonBase
|
|
184
|
rootNode = classification.getRootNode();
|
|
185
|
Pager<IdentifiedEntityDTO<TaxonBase>> tbPager = taxonService.findByIdentifier(TaxonBase.class, "ext-1234", null, rootNode, MatchMode.EXACT, false, null, null, null);
|
|
186
|
Assert.assertEquals("Result size for 'ext' should be 1", Long.valueOf(1), tbPager.getCount());
|
|
187
|
Assert.assertEquals("Result size for 'ext' should be 1", 1, tbPager.getRecords().size());
|
|
188
|
|
|
189
|
tbPager = taxonService.findByIdentifier(TaxonBase.class, "ext-cache1", null, rootNode, MatchMode.EXACT, false, null, null, null);
|
|
190
|
Assert.assertEquals("Result size for 'ext' should be 0", Long.valueOf(0), tbPager.getCount());
|
|
191
|
Assert.assertEquals("Result size for 'ext' should be 0", 0, tbPager.getRecords().size());
|
|
192
|
|
|
193
|
//Synonym
|
|
194
|
Pager<IdentifiedEntityDTO<Synonym>> synPager = taxonService.findByIdentifier(Synonym.class, "ext-syn", null, rootNode, MatchMode.BEGINNING, false, null, null, null);
|
|
195
|
Assert.assertEquals("1 Synonym should be linked to the according classification", Long.valueOf(1), synPager.getCount());
|
|
196
|
Assert.assertEquals("1 Synonym should be linked to the according classification", 1, synPager.getRecords().size());
|
|
197
|
|
|
198
|
}
|
|
199
|
|
|
200
|
@Test
|
|
201
|
@DataSet(value="IdentifiableServiceBaseTest.testFindByIdentifierOrMarker.xml")
|
|
202
|
public final void testFindByMarker(){
|
|
203
|
//classification Filter
|
|
204
|
Classification classification = classificationService.find(5000);
|
|
205
|
TaxonNode rootNode = classification.getRootNode();
|
|
206
|
Boolean markerValue = true;
|
|
207
|
|
|
208
|
UUID uuidMarkerTypeCompleted = MarkerType.uuidComplete;
|
|
209
|
UUID uuidMarkerTypeDoubtful = UUID.fromString("b51325c8-05fe-421a-832b-d86fc249ef6e");
|
|
210
|
|
|
211
|
MarkerType markerType1 = (MarkerType)termService.find(uuidMarkerTypeCompleted);
|
|
212
|
MarkerType noMarkerType = null;
|
|
213
|
MarkerType markerType2 = (MarkerType)termService.find(uuidMarkerTypeDoubtful);
|
|
214
|
Assert.assertNotNull(markerType2);
|
|
215
|
|
|
216
|
TaxonTitleType titleType = TaxonTitleType.TAXON;
|
|
217
|
|
|
218
|
MarkerType markerType = markerType1;
|
|
219
|
Pager<MarkedEntityDTO<Taxon>> taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue,
|
|
220
|
rootNode, true, titleType, null, null, null);
|
|
221
|
Assert.assertEquals("Result size for 'marker1=true' should be 1", Long.valueOf(1), taxonPager.getCount());
|
|
222
|
Assert.assertEquals("Result size for 'marker1=true' should be 1", 1, taxonPager.getRecords().size());
|
|
223
|
MarkedEntityDTO<Taxon> dto = taxonPager.getRecords().get(0);
|
|
224
|
MarkedEntityDTO<Taxon>.Marker marker = dto.getMarker();
|
|
225
|
Assert.assertTrue("Flag must be true", marker.getFlag());
|
|
226
|
Assert.assertEquals("Flag must be true", uuidMarkerTypeCompleted, marker.getTypeUuid());
|
|
227
|
Assert.assertNotNull("the CDM entity in the dto must not be empty if includeEntity=true", dto.getCdmEntity().getEntity());
|
|
228
|
Assert.assertEquals(5000, dto.getCdmEntity().getEntity().getId());
|
|
229
|
|
|
230
|
|
|
231
|
markerValue = false;
|
|
232
|
taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
233
|
Assert.assertEquals("Result size for 'marker1=false' should be 0", Long.valueOf(0), taxonPager.getCount());
|
|
234
|
|
|
235
|
markerValue = true;
|
|
236
|
markerType = noMarkerType;
|
|
237
|
taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
238
|
Assert.assertEquals("Result size for not existing marker type should be 0", Long.valueOf(0), taxonPager.getCount());
|
|
239
|
|
|
240
|
markerType = markerType2;
|
|
241
|
taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
242
|
Assert.assertEquals("Result size for markerType2 should be 0", Long.valueOf(0), taxonPager.getCount());
|
|
243
|
|
|
244
|
rootNode = null;
|
|
245
|
markerType = markerType1;
|
|
246
|
taxonPager = taxonService.findByMarker(Taxon.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
247
|
Assert.assertEquals("Result size for no subtree should be 2", Long.valueOf(2), taxonPager.getCount());
|
|
248
|
|
|
249
|
Pager<MarkedEntityDTO<TaxonBase>> taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
250
|
Assert.assertEquals("Result size for taxa and synonyms without subtree filter with flag = true should be 3", Long.valueOf(3), taxonBasePager.getCount());
|
|
251
|
|
|
252
|
markerValue = null;
|
|
253
|
taxonBasePager = taxonService.findByMarker(TaxonBase.class, markerType, markerValue, rootNode, false, titleType, null, null, null);
|
|
254
|
Assert.assertEquals("Result size for taxa and synonyms without subtree filter with any flag value should be 4", Long.valueOf(4), taxonBasePager.getCount());
|
|
255
|
|
|
256
|
markerValue = true;
|
|
257
|
Pager<MarkedEntityDTO<TaxonName>> namePager = nameService.findByMarker(TaxonName.class, markerType, markerValue, false, null, null, null);
|
|
258
|
Assert.assertEquals("Result size for names with flag = true should be 1", Long.valueOf(1), namePager.getCount());
|
|
259
|
|
|
260
|
}
|
|
261
|
|
|
262
|
|
|
263
|
|
|
264
|
// @Test
|
|
265
|
@Override
|
|
266
|
public void createTestDataSet() throws FileNotFoundException {
|
|
267
|
TermVocabulary<DefinedTerm> voc = vocService.find(VocabularyEnum.IdentifierType.getUuid());
|
|
268
|
|
|
269
|
DefinedTerm identifierType1 = DefinedTerm.NewIdentifierTypeInstance(null, "identifierType1", null);
|
|
270
|
voc.addTerm(identifierType1);
|
|
271
|
termService.save(identifierType1);
|
|
272
|
DefinedTerm identifierType2 = DefinedTerm.NewIdentifierTypeInstance(null, "identifierType2", null);
|
|
273
|
voc.addTerm(identifierType2);
|
|
274
|
termService.save(identifierType2);
|
|
275
|
|
|
276
|
|
|
277
|
IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
|
278
|
Taxon tb = Taxon.NewInstance(name, null);
|
|
279
|
tb.addIdentifier("ext-1234", identifierType1);
|
|
280
|
name.addIdentifier("ext-name12", identifierType2);
|
|
281
|
taxonService.saveOrUpdate(tb);
|
|
282
|
|
|
283
|
Taxon tb2 = Taxon.NewInstance(null, null);
|
|
284
|
tb2.setTitleCache("Cached taxon", true);
|
|
285
|
tb2.addIdentifier("ext-cache1", identifierType2);
|
|
286
|
taxonService.saveOrUpdate(tb2);
|
|
287
|
|
|
288
|
Classification classification = Classification.NewInstance("My classification");
|
|
289
|
classification.addChildTaxon(tb, null, null);
|
|
290
|
classificationService.saveOrUpdate(classification);
|
|
291
|
|
|
292
|
tb2.addSynonymName(null, SynonymType.HOMOTYPIC_SYNONYM_OF());
|
|
293
|
|
|
294
|
commitAndStartNewTransaction(null);
|
|
295
|
|
|
296
|
// this will write flat xml file to the same package in the test resources
|
|
297
|
// the test file is named after the test class like: TestClassName.xml
|
|
298
|
writeDbUnitDataSetFile(new String[] {
|
|
299
|
"TAXONBASE", "TAXONNAME","IDENTIFIER","TAXONBASE_IDENTIFIER",
|
|
300
|
"TAXONNAME_IDENTIFIER",
|
|
301
|
"REFERENCE",
|
|
302
|
"CLASSIFICATION", "TAXONNODE",
|
|
303
|
"HOMOTYPICALGROUP",
|
|
304
|
"TERMVOCABULARY"
|
|
305
|
}, "xxxx");
|
|
306
|
|
|
307
|
}
|
|
308
|
|
|
309
|
|
|
310
|
}
|