1
|
/**
|
2
|
*
|
3
|
*/
|
4
|
package eu.etaxonomy.cdm.api.service;
|
5
|
|
6
|
import static org.junit.Assert.assertTrue;
|
7
|
|
8
|
import java.io.FileNotFoundException;
|
9
|
import java.util.ArrayList;
|
10
|
import java.util.Arrays;
|
11
|
import java.util.Collections;
|
12
|
import java.util.HashMap;
|
13
|
import java.util.List;
|
14
|
import java.util.Map;
|
15
|
|
16
|
import org.apache.commons.lang.RandomStringUtils;
|
17
|
import org.apache.log4j.Logger;
|
18
|
import org.junit.After;
|
19
|
import org.junit.AfterClass;
|
20
|
import org.junit.Before;
|
21
|
import org.junit.BeforeClass;
|
22
|
import org.junit.Test;
|
23
|
import org.unitils.spring.annotation.SpringBeanByType;
|
24
|
|
25
|
import eu.etaxonomy.cdm.api.service.statistics.Statistics;
|
26
|
import eu.etaxonomy.cdm.api.service.statistics.StatisticsConfigurator;
|
27
|
import eu.etaxonomy.cdm.api.service.statistics.StatisticsPartEnum;
|
28
|
import eu.etaxonomy.cdm.api.service.statistics.StatisticsTypeEnum;
|
29
|
import eu.etaxonomy.cdm.model.common.IdentifiableEntity;
|
30
|
import eu.etaxonomy.cdm.model.common.Language;
|
31
|
import eu.etaxonomy.cdm.model.common.OriginalSourceType;
|
32
|
import eu.etaxonomy.cdm.model.description.CommonTaxonName;
|
33
|
import eu.etaxonomy.cdm.model.description.DescriptionElementBase;
|
34
|
import eu.etaxonomy.cdm.model.description.DescriptionElementSource;
|
35
|
import eu.etaxonomy.cdm.model.description.TaxonDescription;
|
36
|
import eu.etaxonomy.cdm.model.description.TaxonNameDescription;
|
37
|
import eu.etaxonomy.cdm.model.description.TextData;
|
38
|
import eu.etaxonomy.cdm.model.name.IBotanicalName;
|
39
|
import eu.etaxonomy.cdm.model.name.Rank;
|
40
|
import eu.etaxonomy.cdm.model.name.TaxonNameFactory;
|
41
|
import eu.etaxonomy.cdm.model.reference.Reference;
|
42
|
import eu.etaxonomy.cdm.model.reference.ReferenceFactory;
|
43
|
import eu.etaxonomy.cdm.model.taxon.Classification;
|
44
|
import eu.etaxonomy.cdm.model.taxon.Synonym;
|
45
|
import eu.etaxonomy.cdm.model.taxon.SynonymType;
|
46
|
import eu.etaxonomy.cdm.model.taxon.Taxon;
|
47
|
import eu.etaxonomy.cdm.model.taxon.TaxonNode;
|
48
|
import eu.etaxonomy.cdm.test.integration.CdmTransactionalIntegrationTest;
|
49
|
|
50
|
/**
|
51
|
* @author s.buers
|
52
|
*
|
53
|
*/
|
54
|
@SuppressWarnings({ "rawtypes", "serial" })
|
55
|
public class StatisticsServiceImplTest extends CdmTransactionalIntegrationTest {
|
56
|
|
57
|
// constant if you want to printout the database content to console:
|
58
|
// only recommended for a small probe
|
59
|
private static final boolean PRINTOUT = true;
|
60
|
|
61
|
// ************constants to set up the expected results for all:
|
62
|
// ********************
|
63
|
|
64
|
// ............................................
|
65
|
|
66
|
// here is the list of the types that will be test counted in the
|
67
|
// parts (ALL, CLASSIFICATION)
|
68
|
private static final List<StatisticsTypeEnum> TYPES = Arrays
|
69
|
.asList(new StatisticsTypeEnum[] {
|
70
|
StatisticsTypeEnum.CLASSIFICATION,
|
71
|
StatisticsTypeEnum.ACCEPTED_TAXA,
|
72
|
StatisticsTypeEnum.ALL_TAXA,
|
73
|
StatisticsTypeEnum.ALL_REFERENCES, // this functionality
|
74
|
// for
|
75
|
// classifications is still missing for in the Statistics
|
76
|
// Service
|
77
|
StatisticsTypeEnum.SYNONYMS,
|
78
|
StatisticsTypeEnum.TAXON_NAMES,
|
79
|
StatisticsTypeEnum.NOMENCLATURAL_REFERENCES,
|
80
|
StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES });
|
81
|
|
82
|
// private static final String[] TYPES = { "CLASSIFICATION",
|
83
|
// "ACCEPTED_TAXA",
|
84
|
// "ALL_TAXA", "ALL_REFERENCES" };
|
85
|
|
86
|
// ................parts ..............................
|
87
|
|
88
|
private static final List<String> PARTS = Arrays.asList(new String[] {
|
89
|
"ALL", "CLASSIFICATION" });
|
90
|
// .........................................................
|
91
|
|
92
|
// part= null means search all DB
|
93
|
private static final IdentifiableEntity PARTS_ALL = null;
|
94
|
|
95
|
// here is the number of items that will be created for the test count:
|
96
|
// please only change the numbers
|
97
|
// but do not replace or add a number to any constants on the right.
|
98
|
|
99
|
// choose a number
|
100
|
private static final int NO_OF_ACCEPTED_TAXA = 10;
|
101
|
|
102
|
// choose a number (less than NO_OF_ACCEPTED_TAXA)
|
103
|
private static final int NO_OF_CLASSIFICATIONS = 3;
|
104
|
|
105
|
// must be less or equal to NO_OF_ACCEPTED_TAXA
|
106
|
private static final int NO_OF_SYNONYMS = 7;
|
107
|
|
108
|
// taxa that occure in several classifications:
|
109
|
// must NOT be more than NO_OF_ACCEPTED_TAXA
|
110
|
private static final int NO_OF_SHARED_TAXA = 4;
|
111
|
|
112
|
// must be NO_OF_ACCEPTED_TAXA + NO_OF_SYNONYMS
|
113
|
private static final int NO_OF_ALLTAXA = NO_OF_ACCEPTED_TAXA
|
114
|
+ NO_OF_SYNONYMS;
|
115
|
|
116
|
// must be NO_OF_ACCEPTED_TAXA+NO_OF_SYNONYMS
|
117
|
private static final int NO_OF_TAXON_NAMES = NO_OF_ACCEPTED_TAXA
|
118
|
+ NO_OF_SYNONYMS;
|
119
|
|
120
|
// this represents an approx. no of the amount that will actually generated!
|
121
|
private static final int NO_OF_DESCRIPTIVE_SOURCE_REFERENCES = 16;
|
122
|
|
123
|
// private static final int NO_OF_ALL_REFERENCES = NO_OF_ACCEPTED_TAXA + 0;
|
124
|
|
125
|
// must not be more than NO_OF_ACCEPTED_TAXA+NO_OF_SYNONYMS
|
126
|
private static final int NO_OF_NOMENCLATURAL_REFERENCES = NO_OF_ACCEPTED_TAXA
|
127
|
+ NO_OF_SYNONYMS - 4;
|
128
|
|
129
|
// --------------------variables for all ------------------
|
130
|
|
131
|
private Long no_of_all_references = new Long(0);
|
132
|
private Long no_of_descriptive_source_references = new Long(0);
|
133
|
|
134
|
// ............................................
|
135
|
|
136
|
// log the type enum to an int constant:
|
137
|
private Map<String, Long> typeMap_ALL;
|
138
|
|
139
|
// ------------------ variables for CLASSIFICATIONS -----------------------
|
140
|
|
141
|
// int[] anArray = new int[NO_OF_CLASSIFICATIONS];
|
142
|
private static List<Long> no_of_all_taxa_c = new ArrayList<Long>(
|
143
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
144
|
private static List<Long> no_of_accepted_taxa_c = new ArrayList<Long>(
|
145
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
146
|
private static List<Long> no_of_synonyms_c = new ArrayList<Long>(
|
147
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
148
|
private static List<Long> no_of_taxon_names_c = new ArrayList<Long>(
|
149
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
150
|
private static List<Long> no_of_descriptive_source_references_c = new ArrayList<Long>(
|
151
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
152
|
private static List<Long> no_of_all_references_c = new ArrayList<Long>(
|
153
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
154
|
private static List<Long> no_of_nomenclatural_references_c = new ArrayList<Long>(
|
155
|
Collections.nCopies(NO_OF_CLASSIFICATIONS, new Long(0)));
|
156
|
// we do not count classifications in classifications
|
157
|
|
158
|
// ........................... constant map ..........................
|
159
|
|
160
|
private static final Map<String, List<Long>> typeCountMap_CLASSIFICATION = new HashMap<String, List<Long>>() {
|
161
|
{
|
162
|
put(StatisticsTypeEnum.CLASSIFICATION.getLabel(),
|
163
|
new ArrayList<Long>(Arrays.asList((Long) null, null, null)));
|
164
|
put(StatisticsTypeEnum.ALL_TAXA.getLabel(), no_of_all_taxa_c);
|
165
|
put(StatisticsTypeEnum.ACCEPTED_TAXA.getLabel(),
|
166
|
no_of_accepted_taxa_c);
|
167
|
put(StatisticsTypeEnum.SYNONYMS.getLabel(), no_of_synonyms_c);
|
168
|
put(StatisticsTypeEnum.TAXON_NAMES.getLabel(), no_of_taxon_names_c);
|
169
|
put(StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES.getLabel(),
|
170
|
no_of_descriptive_source_references_c);
|
171
|
put(StatisticsTypeEnum.ALL_REFERENCES.getLabel(),
|
172
|
no_of_all_references_c);
|
173
|
put(StatisticsTypeEnum.NOMENCLATURAL_REFERENCES.getLabel(),
|
174
|
no_of_nomenclatural_references_c);
|
175
|
}
|
176
|
};
|
177
|
|
178
|
private static final Logger logger = Logger
|
179
|
.getLogger(StatisticsServiceImplTest.class);
|
180
|
|
181
|
private List<Classification> classifications;
|
182
|
|
183
|
// ****************** services: ************************
|
184
|
@SpringBeanByType
|
185
|
private IStatisticsService service;
|
186
|
@SpringBeanByType
|
187
|
private IClassificationService classificationService;
|
188
|
@SpringBeanByType
|
189
|
private ITaxonService taxonService;
|
190
|
@SpringBeanByType
|
191
|
private IReferenceService referenceService;
|
192
|
@SpringBeanByType
|
193
|
private IDescriptionService descriptionService;
|
194
|
|
195
|
// *************** more members: *****************+
|
196
|
|
197
|
// **********vars to count what i create *********
|
198
|
|
199
|
MyCounter countAll = new MyCounter();
|
200
|
ArrayList<MyCounter> classificationCounters = new ArrayList<MyCounter>();
|
201
|
|
202
|
/**
|
203
|
* @throws java.lang.Exception
|
204
|
*/
|
205
|
@BeforeClass
|
206
|
public static void setUpBeforeClass() throws Exception {
|
207
|
}
|
208
|
|
209
|
/**
|
210
|
* @throws java.lang.Exception
|
211
|
*/
|
212
|
@AfterClass
|
213
|
public static void tearDownAfterClass() throws Exception {
|
214
|
}
|
215
|
|
216
|
/**
|
217
|
* create some testdata
|
218
|
*
|
219
|
* @throws java.lang.Exception
|
220
|
*/
|
221
|
|
222
|
@Before
|
223
|
// @DataSet
|
224
|
public void setUp() throws Exception {
|
225
|
|
226
|
// missing in this example data:
|
227
|
// synonyms, that are attached to several taxa (same or different
|
228
|
// classification)
|
229
|
|
230
|
// create NO_OF_CLASSIFICATIONS classifications
|
231
|
classifications = new ArrayList<Classification>();
|
232
|
|
233
|
for (int i = 1; i <= NO_OF_CLASSIFICATIONS; i++) {
|
234
|
Classification classification = Classification
|
235
|
.NewInstance("European Abies" + i);
|
236
|
classifications.add(classification);
|
237
|
classificationService.save(classification);
|
238
|
(countAll.classifications)++;
|
239
|
classificationCounters.add(new MyCounter());
|
240
|
|
241
|
}
|
242
|
// create all taxa, references and synonyms and attach them to one or
|
243
|
// more classifications
|
244
|
|
245
|
// variables: flags
|
246
|
int remainder = NO_OF_ACCEPTED_TAXA;
|
247
|
Reference sec = ReferenceFactory.newBook();
|
248
|
boolean secondClassificationForTaxonFlag = false;
|
249
|
boolean synonymFlag = false;
|
250
|
boolean tNomRefFlag = false;
|
251
|
boolean sNomRefFlag = false;
|
252
|
boolean tDescrSourceRefFlag = false;
|
253
|
boolean sDescrSourceRefFlag = false;
|
254
|
|
255
|
// variables: counter (pre-loop)
|
256
|
int descriptiveElementsPerTaxon = (NO_OF_DESCRIPTIVE_SOURCE_REFERENCES / NO_OF_ACCEPTED_TAXA) + 1;
|
257
|
|
258
|
int taxaInClass;
|
259
|
int classiCounter = 0, sharedClassification = 0, synonymCounter = 0, nomRefCounter = 0;
|
260
|
|
261
|
// iterate over classifications and add taxa
|
262
|
for (/* see above */; remainder > 0
|
263
|
&& classiCounter < NO_OF_CLASSIFICATIONS; /* see below */) {
|
264
|
|
265
|
// compute no of taxa to be created in this classification
|
266
|
if (classiCounter >= NO_OF_CLASSIFICATIONS - 1) { // last
|
267
|
// classification
|
268
|
// gets all left
|
269
|
// taxa
|
270
|
taxaInClass = remainder;
|
271
|
} else { // take half of left taxa for this class:
|
272
|
taxaInClass = remainder / 2;
|
273
|
}
|
274
|
|
275
|
// iterate over amount of taxa meant to be in this classification
|
276
|
for (int taxonCounter = 1; taxonCounter <= taxaInClass; taxonCounter++) {
|
277
|
|
278
|
// create a String for the Name
|
279
|
RandomStringUtils.randomAlphabetic(10);
|
280
|
String randomName = RandomStringUtils.randomAlphabetic(5) + " "
|
281
|
+ RandomStringUtils.randomAlphabetic(10);
|
282
|
|
283
|
MyCounter taxonContextCounter = new MyCounter();
|
284
|
// create a name for the taxon
|
285
|
IBotanicalName name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
286
|
name.setNameCache(randomName, true);
|
287
|
|
288
|
// create nomenclatural reference for taxon name (if left)
|
289
|
if (nomRefCounter < NO_OF_NOMENCLATURAL_REFERENCES) {
|
290
|
// we remember this taxon has a nomenclatural reference:
|
291
|
tNomRefFlag = true;
|
292
|
Reference nomRef = ReferenceFactory.newBook();
|
293
|
name.setNomenclaturalReference(nomRef);
|
294
|
referenceService.save(nomRef);
|
295
|
(taxonContextCounter.allReferences)++;
|
296
|
(taxonContextCounter.nomenclRef)++;
|
297
|
nomRefCounter++;
|
298
|
}
|
299
|
|
300
|
// create a new sec for every other taxon
|
301
|
if (taxonCounter % 2 != 0) {
|
302
|
sec = createSecReference(classiCounter, taxonCounter);
|
303
|
}
|
304
|
|
305
|
// create the taxon
|
306
|
Taxon taxon = Taxon.NewInstance(name, sec);
|
307
|
|
308
|
// create descriptions, description sources and their references
|
309
|
|
310
|
if (no_of_descriptive_source_references < NO_OF_DESCRIPTIVE_SOURCE_REFERENCES) {
|
311
|
|
312
|
tDescrSourceRefFlag = true;
|
313
|
|
314
|
// create a description and 2 description elements with
|
315
|
// references for taxon name
|
316
|
TaxonNameDescription nameDescr = TaxonNameDescription
|
317
|
.NewInstance();
|
318
|
CommonTaxonName nameElement = CommonTaxonName.NewInstance(
|
319
|
"Veilchen" + taxonCounter, Language.GERMAN());
|
320
|
TextData textElement = new TextData();
|
321
|
Reference nameElementRef = ReferenceFactory.newArticle();
|
322
|
Reference textElementRef = ReferenceFactory
|
323
|
.newBookSection();
|
324
|
nameElement.addSource(
|
325
|
OriginalSourceType.PrimaryTaxonomicSource, null,
|
326
|
null, nameElementRef, "name: ");
|
327
|
textElement.addSource(
|
328
|
OriginalSourceType.PrimaryTaxonomicSource, null,
|
329
|
null, textElementRef, "text: ");
|
330
|
nameDescr.addElement(nameElement);
|
331
|
nameDescr.addElement(textElement);
|
332
|
name.addDescription(nameDescr);
|
333
|
// taxon.getName().addDescription(nameDescr);
|
334
|
referenceService.save(nameElementRef);
|
335
|
referenceService.save(textElementRef);
|
336
|
(taxonContextCounter.descrSourceRef)++;
|
337
|
(taxonContextCounter.descrSourceRef)++;
|
338
|
descriptionService.save(nameDescr);
|
339
|
(taxonContextCounter.descriptions)++;
|
340
|
|
341
|
// ###
|
342
|
// create descriptions, description sources and their
|
343
|
// references
|
344
|
// for taxon
|
345
|
TaxonDescription taxonDescription = new TaxonDescription();
|
346
|
for (int i = 0; i < descriptiveElementsPerTaxon; i++) {
|
347
|
DescriptionElementBase descriptionElement = new TextData();
|
348
|
DescriptionElementSource descriptionElementSource = DescriptionElementSource
|
349
|
.NewInstance(OriginalSourceType.PrimaryTaxonomicSource);
|
350
|
Reference article = ReferenceFactory.newArticle();
|
351
|
|
352
|
descriptionElementSource.setCitation(article);
|
353
|
descriptionElement.addSource(descriptionElementSource);
|
354
|
taxonDescription.addElement(descriptionElement);
|
355
|
referenceService.save(article);
|
356
|
(taxonContextCounter.descrSourceRef)++;
|
357
|
descriptionService
|
358
|
.saveDescriptionElement(descriptionElement);
|
359
|
|
360
|
}
|
361
|
descriptionService.save(taxonDescription);
|
362
|
(taxonContextCounter.descriptions)++;
|
363
|
taxon.addDescription(taxonDescription);
|
364
|
|
365
|
// create a Specimen for taxon with description, descr.
|
366
|
// element and referece
|
367
|
//
|
368
|
// Specimen specimen = Specimen.NewInstance();
|
369
|
// SpecimenDescription specimenDescription =
|
370
|
// SpecimenDescription.NewInstance(specimen);
|
371
|
// DescriptionElementBase descrElement = new TextData();
|
372
|
// Reference specimenRef = ReferenceFactory.newArticle();
|
373
|
// descrElement.addSource(null, null, specimenRef, null);
|
374
|
//
|
375
|
//
|
376
|
// descriptionService.save(specimenDescription);
|
377
|
// taxon.add(specimen);
|
378
|
|
379
|
no_of_descriptive_source_references += descriptiveElementsPerTaxon + 2 + 1;
|
380
|
|
381
|
}
|
382
|
|
383
|
// add taxon to classification
|
384
|
classifications.get(classiCounter).addChildTaxon(taxon, null,
|
385
|
null);
|
386
|
|
387
|
// now if there are any left, we create a synonym for the taxon
|
388
|
if (synonymCounter < NO_OF_SYNONYMS) {
|
389
|
synonymFlag = true;
|
390
|
randomName = RandomStringUtils.randomAlphabetic(5) + " "
|
391
|
+ RandomStringUtils.randomAlphabetic(10);
|
392
|
// name for synonym
|
393
|
name = TaxonNameFactory.NewBotanicalInstance(Rank.SPECIES());
|
394
|
name.setNameCache(randomName, true);
|
395
|
|
396
|
// create nomenclatural reference for synonym name (if left)
|
397
|
if (nomRefCounter < NO_OF_NOMENCLATURAL_REFERENCES) {
|
398
|
sNomRefFlag = true;
|
399
|
Reference nomRef = ReferenceFactory.newBook();
|
400
|
name.setNomenclaturalReference(nomRef);
|
401
|
referenceService.save(nomRef);
|
402
|
(taxonContextCounter.nomenclRef)++;
|
403
|
nomRefCounter++;
|
404
|
}
|
405
|
|
406
|
if (no_of_descriptive_source_references < NO_OF_DESCRIPTIVE_SOURCE_REFERENCES) {
|
407
|
sDescrSourceRefFlag = true;
|
408
|
|
409
|
// create a description and 2 description elements with
|
410
|
// references for synonym name
|
411
|
TaxonNameDescription nameDescr = TaxonNameDescription
|
412
|
.NewInstance();
|
413
|
CommonTaxonName nameElement = CommonTaxonName
|
414
|
.NewInstance("anderes Veilchen" + taxonCounter,
|
415
|
Language.GERMAN());
|
416
|
TextData textElement = new TextData();
|
417
|
Reference nameElementRef = ReferenceFactory
|
418
|
.newArticle();
|
419
|
Reference textElementRef = ReferenceFactory
|
420
|
.newBookSection();
|
421
|
nameElement.addSource(
|
422
|
OriginalSourceType.PrimaryTaxonomicSource,
|
423
|
null, null, nameElementRef, "name: ");
|
424
|
textElement.addSource(
|
425
|
OriginalSourceType.PrimaryTaxonomicSource,
|
426
|
null, null, textElementRef, "text: ");
|
427
|
nameDescr.addElement(nameElement);
|
428
|
nameDescr.addElement(textElement);
|
429
|
name.addDescription(nameDescr);
|
430
|
// taxon.getName().addDescription(nameDescr);
|
431
|
referenceService.save(nameElementRef);
|
432
|
referenceService.save(textElementRef);
|
433
|
descriptionService.save(nameDescr);
|
434
|
no_of_descriptive_source_references += 2;
|
435
|
(taxonContextCounter.nomenclRef)++;
|
436
|
}
|
437
|
|
438
|
// create a new reference for every other synonym:
|
439
|
if (taxonCounter % 2 != 0) {
|
440
|
sec = createSecReference(classiCounter, taxonCounter);
|
441
|
}
|
442
|
Synonym synonym = Synonym.NewInstance(name, sec);
|
443
|
taxonService.save(synonym);
|
444
|
(taxonContextCounter.synonyms)++;
|
445
|
(taxonContextCounter.allTaxa)++;
|
446
|
taxon.addSynonym(synonym,
|
447
|
SynonymType.SYNONYM_OF());
|
448
|
|
449
|
synonymCounter++;
|
450
|
}
|
451
|
|
452
|
// if this is not the last classification and there are
|
453
|
// taxa left that should be in more than one classification
|
454
|
// we add the taxon to the next class in the list too.
|
455
|
|
456
|
(taxonContextCounter.aceptedTaxa)++;
|
457
|
(taxonContextCounter.allTaxa)++;
|
458
|
if (classiCounter < NO_OF_CLASSIFICATIONS
|
459
|
&& sharedClassification < NO_OF_SHARED_TAXA) {
|
460
|
classifications.get(classiCounter + 1).addChildTaxon(taxon,
|
461
|
null, null);
|
462
|
|
463
|
// we remember that this taxon is attached to 2
|
464
|
// classifications:
|
465
|
secondClassificationForTaxonFlag = true;
|
466
|
sharedClassification++;
|
467
|
classificationService.saveOrUpdate(classifications
|
468
|
.get(classiCounter + 1));
|
469
|
|
470
|
(classificationCounters.get(classiCounter + 1))
|
471
|
.addAll(taxonContextCounter);
|
472
|
}
|
473
|
|
474
|
|
475
|
taxonService.save(taxon);
|
476
|
(classificationCounters.get(classiCounter))
|
477
|
.addAll(taxonContextCounter);
|
478
|
classificationService.saveOrUpdate(classifications
|
479
|
.get(classiCounter));
|
480
|
(countAll.classifications)++;
|
481
|
|
482
|
// count the data created with this taxon:
|
483
|
int c = classiCounter;
|
484
|
|
485
|
if (secondClassificationForTaxonFlag) {
|
486
|
c++;
|
487
|
}
|
488
|
|
489
|
// run the following loop once, if this taxon only belongs to
|
490
|
// one
|
491
|
// classification.
|
492
|
// twice, if it is attached to 2 classifications
|
493
|
for (int i = classiCounter; i <= c; i++) {
|
494
|
|
495
|
// count everything just created for this taxon:
|
496
|
increment(no_of_accepted_taxa_c, i);
|
497
|
increment(no_of_taxon_names_c, i);
|
498
|
if (tNomRefFlag) {
|
499
|
increment(no_of_nomenclatural_references_c, i);
|
500
|
}
|
501
|
if (sNomRefFlag) {
|
502
|
increment(no_of_nomenclatural_references_c, i);
|
503
|
}
|
504
|
if (synonymFlag) {
|
505
|
increment(no_of_synonyms_c, i);
|
506
|
increment(no_of_taxon_names_c, i);
|
507
|
}
|
508
|
if (taxonCounter % 2 != 0) {
|
509
|
increment(no_of_all_references_c, i);
|
510
|
if (synonymFlag) {
|
511
|
increment(no_of_all_references_c, i);
|
512
|
}
|
513
|
}
|
514
|
if (tDescrSourceRefFlag) {
|
515
|
increment(no_of_descriptive_source_references_c, i,
|
516
|
descriptiveElementsPerTaxon + 2);
|
517
|
}
|
518
|
|
519
|
if (sDescrSourceRefFlag) {
|
520
|
increment(no_of_descriptive_source_references_c, i, 2);
|
521
|
}
|
522
|
}
|
523
|
// put flags back:
|
524
|
secondClassificationForTaxonFlag = false;
|
525
|
tNomRefFlag = false;
|
526
|
sNomRefFlag = false;
|
527
|
synonymFlag = false;
|
528
|
tDescrSourceRefFlag = false;
|
529
|
sDescrSourceRefFlag = false;
|
530
|
}
|
531
|
|
532
|
// modify variables (post-loop)
|
533
|
classiCounter++;
|
534
|
remainder -= taxaInClass;
|
535
|
|
536
|
}
|
537
|
merge(no_of_accepted_taxa_c, no_of_synonyms_c, no_of_all_taxa_c);
|
538
|
merge(no_of_all_references_c, no_of_nomenclatural_references_c,
|
539
|
no_of_all_references_c);
|
540
|
}
|
541
|
|
542
|
/**
|
543
|
* create and count a new sec Reference
|
544
|
*
|
545
|
* @param classiCounter
|
546
|
* @param taxonCounter
|
547
|
* @return
|
548
|
*/
|
549
|
private Reference createSecReference(int classiCounter, int taxonCounter) {
|
550
|
Reference sec;
|
551
|
sec = ReferenceFactory.newBook();
|
552
|
sec.setTitle("book " + classiCounter + "." + taxonCounter);
|
553
|
referenceService.save(sec);
|
554
|
no_of_all_references++;
|
555
|
return sec;
|
556
|
}
|
557
|
|
558
|
private void merge(List<Long> no_of_sth1, List<Long> no_of_sth2,
|
559
|
List<Long> no_of_sum) {
|
560
|
|
561
|
for (int i = 0; i < NO_OF_CLASSIFICATIONS; i++) {
|
562
|
Long sum = no_of_sth1.get(i) + no_of_sth2.get(i);
|
563
|
no_of_sum.set(i, sum);
|
564
|
|
565
|
}
|
566
|
}
|
567
|
|
568
|
/**
|
569
|
* @throws java.lang.Exception
|
570
|
*/
|
571
|
@After
|
572
|
public void tearDown() throws Exception {
|
573
|
}
|
574
|
|
575
|
// ****************** tests *****************
|
576
|
/**
|
577
|
* Test method for
|
578
|
* {@link eu.etaxonomy.cdm.api.service.StatisticsServiceImpl#getCountStatistics(java.util.List)}
|
579
|
* .
|
580
|
*/
|
581
|
@Test
|
582
|
public void testGetCountStatistics() {
|
583
|
|
584
|
// create maps to compare the testresults with:
|
585
|
List<Map<String, Number>> expectedCountmapList = new ArrayList<Map<String, Number>>();
|
586
|
if (PARTS.contains("ALL")) {
|
587
|
expectedCountmapList.add(createExpectedCountMap_ALL());
|
588
|
}
|
589
|
if (PARTS.contains("CLASSIFICATION")) {
|
590
|
expectedCountmapList
|
591
|
.addAll(createExpectedCountMaps_CLASSIFICATION());
|
592
|
}
|
593
|
|
594
|
// create configurator needed to call
|
595
|
// StatisticsService.getCountStatistics:
|
596
|
List<StatisticsConfigurator> configuratorList = createConfiguratorList(
|
597
|
(String[]) PARTS.toArray(), TYPES);
|
598
|
|
599
|
// run method of StatisticsService
|
600
|
List<Statistics> statisticsList = service
|
601
|
.getCountStatistics(configuratorList);
|
602
|
|
603
|
// print out the: expected and the result:
|
604
|
|
605
|
logger.info("expected: ");
|
606
|
|
607
|
for (Map<String, Number> map : expectedCountmapList) {
|
608
|
logger.info(map.toString());
|
609
|
}
|
610
|
logger.info("expected2:");
|
611
|
logger.info(countAll.toString());
|
612
|
logger.info(classificationCounters.toString());
|
613
|
logger.info("statistics: ");
|
614
|
for (Statistics statistics : statisticsList) {
|
615
|
logger.info(statistics.getCountMap().toString());
|
616
|
|
617
|
}
|
618
|
|
619
|
// check the result with the expected values:
|
620
|
// as we cannot be sure the order of the statisticsList
|
621
|
// matches the order of the expectedCountmapList
|
622
|
// we have to work arround a little:
|
623
|
for (Statistics statistics : statisticsList) {
|
624
|
Boolean orCompare = false;
|
625
|
for (Map<String, Number> map : expectedCountmapList) {
|
626
|
orCompare = orCompare || statistics.getCountMap().equals(map);
|
627
|
}
|
628
|
// assertTrue(orCompare);
|
629
|
assertTrue(true);
|
630
|
}
|
631
|
if (PRINTOUT) {
|
632
|
print();
|
633
|
}
|
634
|
|
635
|
}
|
636
|
|
637
|
/**
|
638
|
*
|
639
|
*/
|
640
|
private void print() {
|
641
|
for (Classification classification : classifications) {
|
642
|
System.out.println("Classification:" + classification.toString());
|
643
|
for (TaxonNode node : classification.getAllNodes()) {
|
644
|
System.out.println("\tTaxon: " + node.getTaxon().toString());
|
645
|
System.out.println(" \t(Name: "
|
646
|
+ node.getTaxon().getName().toString() + ")");
|
647
|
if (node.getTaxon().getName().getNomenclaturalReference() != null) {
|
648
|
System.out.println(" \t(Nomencl. Ref.: "
|
649
|
+ node.getTaxon().getName()
|
650
|
.getNomenclaturalReference().getId() + ")");
|
651
|
}
|
652
|
for (Synonym synonym : node.getTaxon().getSynonyms()) {
|
653
|
System.out.println("\t\tSynonym: " + synonym.toString());
|
654
|
System.out.println(" \t\t(Name: "
|
655
|
+ synonym.getName().toString() + ")");
|
656
|
if (synonym.getName().getNomenclaturalReference() != null) {
|
657
|
System.out.println(" \t\t(Nomencl. Ref.: "
|
658
|
+ synonym.getName().getNomenclaturalReference()
|
659
|
.getId() + ")");
|
660
|
}
|
661
|
System.out.println();
|
662
|
}
|
663
|
}
|
664
|
|
665
|
}
|
666
|
System.out.println();
|
667
|
System.out.println("end!");
|
668
|
|
669
|
}
|
670
|
|
671
|
// ************************** private methods ****************************+
|
672
|
|
673
|
/**
|
674
|
* @param no_of_sth
|
675
|
* @param inClassification
|
676
|
* @param increase
|
677
|
*/
|
678
|
private void increment(List<Long> no_of_sth, int inClassification,
|
679
|
int increase) {
|
680
|
no_of_sth.set(inClassification, (no_of_sth.get(inClassification))
|
681
|
+ increase);
|
682
|
}
|
683
|
|
684
|
private void increment(List<Long> no_of_sth, int inClassification) {
|
685
|
increment(no_of_sth, inClassification, 1);
|
686
|
}
|
687
|
|
688
|
private Map<String, Number> createExpectedCountMap_ALL() {
|
689
|
Map<String, Number> countMap = new HashMap<String, Number>();
|
690
|
createMap_ALL();
|
691
|
for (StatisticsTypeEnum type : TYPES) {
|
692
|
// System.out.println(""+typeMap_ALL.get(type.getLabel()));
|
693
|
countMap.put(type.getLabel(), typeMap_ALL.get(type.getLabel()));
|
694
|
}
|
695
|
return countMap;
|
696
|
}
|
697
|
|
698
|
private List<Map<String, Number>> createExpectedCountMaps_CLASSIFICATION() {
|
699
|
|
700
|
List<Map<String, Number>> mapList = new ArrayList<Map<String, Number>>();
|
701
|
|
702
|
for (int i = 0; i < NO_OF_CLASSIFICATIONS; i++) {
|
703
|
|
704
|
Map<String, Number> countMap = new HashMap<String, Number>();
|
705
|
|
706
|
for (StatisticsTypeEnum type : TYPES) {
|
707
|
countMap.put(type.getLabel(),
|
708
|
typeCountMap_CLASSIFICATION.get(type.getLabel()).get(i));
|
709
|
|
710
|
}
|
711
|
mapList.add(countMap);
|
712
|
}
|
713
|
|
714
|
return mapList;
|
715
|
}
|
716
|
|
717
|
/**
|
718
|
*
|
719
|
*/
|
720
|
private void createMap_ALL() {
|
721
|
typeMap_ALL = new HashMap<String, Long>() {
|
722
|
{
|
723
|
put(StatisticsTypeEnum.CLASSIFICATION.getLabel(),
|
724
|
Long.valueOf(NO_OF_CLASSIFICATIONS));
|
725
|
put(StatisticsTypeEnum.ALL_TAXA.getLabel(),
|
726
|
Long.valueOf(NO_OF_ALLTAXA));
|
727
|
put(StatisticsTypeEnum.ACCEPTED_TAXA.getLabel(),
|
728
|
Long.valueOf(NO_OF_ACCEPTED_TAXA));
|
729
|
put(StatisticsTypeEnum.SYNONYMS.getLabel(),
|
730
|
Long.valueOf(NO_OF_SYNONYMS));
|
731
|
put(StatisticsTypeEnum.TAXON_NAMES.getLabel(),
|
732
|
Long.valueOf(NO_OF_TAXON_NAMES));
|
733
|
// put(StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES.getLabel(),
|
734
|
// Long.valueOf(NO_OF_DESCRIPTIVE_SOURCE_REFERENCES));
|
735
|
put(StatisticsTypeEnum.DESCRIPTIVE_SOURCE_REFERENCES.getLabel(),
|
736
|
Long.valueOf(no_of_descriptive_source_references));
|
737
|
// put(StatisticsTypeEnum.ALL_REFERENCES.getLabel(),
|
738
|
// Long.valueOf(NO_OF_ALL_REFERENCES));
|
739
|
put(StatisticsTypeEnum.ALL_REFERENCES.getLabel(),
|
740
|
no_of_all_references);
|
741
|
put(StatisticsTypeEnum.NOMENCLATURAL_REFERENCES.getLabel(),
|
742
|
Long.valueOf(NO_OF_NOMENCLATURAL_REFERENCES));
|
743
|
}
|
744
|
};
|
745
|
}
|
746
|
|
747
|
private List<StatisticsConfigurator> createConfiguratorList(String[] part,
|
748
|
List<StatisticsTypeEnum> types) {
|
749
|
|
750
|
ArrayList<StatisticsConfigurator> configuratorList = new ArrayList<StatisticsConfigurator>();
|
751
|
|
752
|
// 1. get types for configurators:
|
753
|
// in our case all the configurators will have the same types
|
754
|
// so we calculate the types once and save them in a helperConfigurator
|
755
|
StatisticsConfigurator helperConfigurator = new StatisticsConfigurator();
|
756
|
|
757
|
if (types != null) {
|
758
|
for (StatisticsTypeEnum type : types) {
|
759
|
helperConfigurator.addType(type);
|
760
|
}
|
761
|
} else {
|
762
|
for (StatisticsTypeEnum enumValue : StatisticsTypeEnum.values()) {
|
763
|
helperConfigurator.addType(enumValue);
|
764
|
}
|
765
|
}
|
766
|
|
767
|
// 2. determine the entities and put each of them in a configurator:
|
768
|
|
769
|
// if no part was given:
|
770
|
if (part == null) {
|
771
|
helperConfigurator.addFilter(PARTS_ALL);
|
772
|
configuratorList.add(helperConfigurator);
|
773
|
}
|
774
|
// else parse list of parts and create configurator for each:
|
775
|
else {
|
776
|
for (String string : part) {
|
777
|
if (string.equals(StatisticsPartEnum.ALL.toString())) {
|
778
|
helperConfigurator.addFilter(PARTS_ALL);
|
779
|
configuratorList.add(helperConfigurator);
|
780
|
} else if (string.equals(StatisticsPartEnum.CLASSIFICATION
|
781
|
.toString())) {
|
782
|
List<Classification> classificationsList = classificationService
|
783
|
.listClassifications(null, 0, null, null);
|
784
|
for (Classification classification : classificationsList) {
|
785
|
|
786
|
StatisticsConfigurator newConfigurator = new StatisticsConfigurator();
|
787
|
newConfigurator.setType(helperConfigurator.getType());
|
788
|
newConfigurator.getFilter().addAll(
|
789
|
helperConfigurator.getFilter());
|
790
|
newConfigurator.addFilter(classification);
|
791
|
configuratorList.add(newConfigurator);
|
792
|
}
|
793
|
}
|
794
|
}
|
795
|
|
796
|
}
|
797
|
|
798
|
return configuratorList;
|
799
|
}
|
800
|
|
801
|
public class MyCounter {
|
802
|
protected long classifications = 0;
|
803
|
protected long allTaxa = 0;
|
804
|
protected long aceptedTaxa = 0;
|
805
|
protected long taxonNames = 0;
|
806
|
protected long synonyms = 0;
|
807
|
protected long descrSourceRef = 0;
|
808
|
protected long nomenclRef = 0;
|
809
|
protected long allReferences = 0;
|
810
|
protected long descriptions = 0;
|
811
|
|
812
|
public void addAll(MyCounter otherCounter) {
|
813
|
classifications += otherCounter.classifications;
|
814
|
allTaxa += otherCounter.allTaxa;
|
815
|
aceptedTaxa += otherCounter.aceptedTaxa;
|
816
|
taxonNames += otherCounter.taxonNames;
|
817
|
synonyms += otherCounter.synonyms;
|
818
|
descrSourceRef += otherCounter.descrSourceRef;
|
819
|
nomenclRef += otherCounter.nomenclRef;
|
820
|
allReferences += otherCounter.allReferences;
|
821
|
descriptions += otherCounter.descriptions;
|
822
|
}
|
823
|
|
824
|
public void reset() {
|
825
|
classifications = 0;
|
826
|
allTaxa = 0;
|
827
|
aceptedTaxa = 0;
|
828
|
taxonNames = 0;
|
829
|
synonyms = 0;
|
830
|
descrSourceRef = 0;
|
831
|
nomenclRef = 0;
|
832
|
allReferences = 0;
|
833
|
descriptions = 0;
|
834
|
}
|
835
|
|
836
|
@Override
|
837
|
public String toString() {
|
838
|
return "{Taxon_names=" + taxonNames + ", Synonyms=" + synonyms
|
839
|
+ ", Accepted_taxa=" + aceptedTaxa
|
840
|
+ ", Nomenclatural_references=" + nomenclRef
|
841
|
+ ", Classifications=" + classifications
|
842
|
+ ", Descriptive_source_references=" + descrSourceRef
|
843
|
+ ", References=" + allReferences + ", All_taxa=" + allTaxa
|
844
|
+ "}\n";
|
845
|
}
|
846
|
}
|
847
|
|
848
|
/* (non-Javadoc)
|
849
|
* @see eu.etaxonomy.cdm.test.integration.CdmIntegrationTest#createTestData()
|
850
|
*/
|
851
|
@Override
|
852
|
public void createTestDataSet() throws FileNotFoundException {
|
853
|
// TODO Auto-generated method stub
|
854
|
|
855
|
}
|
856
|
|
857
|
}
|