-
Notifications
You must be signed in to change notification settings - Fork 171
/
Copy pathCcServiceImpl.java
1444 lines (1274 loc) · 73.8 KB
/
CcServiceImpl.java
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
package org.ohdsi.webapi.cohortcharacterization;
import com.cosium.spring.data.jpa.entity.graph.domain.EntityGraph;
import com.fasterxml.jackson.core.type.TypeReference;
import com.google.common.collect.ImmutableList;
import org.apache.commons.io.FileUtils;
import org.apache.commons.lang3.StringUtils;
import org.ohdsi.analysis.Utils;
import org.ohdsi.analysis.WithId;
import org.ohdsi.analysis.cohortcharacterization.design.CohortCharacterization;
import org.ohdsi.analysis.cohortcharacterization.design.StandardFeatureAnalysisType;
import org.ohdsi.circe.helper.ResourceHelper;
import org.ohdsi.featureExtraction.FeatureExtraction;
import org.ohdsi.hydra.Hydra;
import org.ohdsi.sql.SqlSplit;
import org.ohdsi.sql.SqlTranslate;
import org.ohdsi.webapi.Constants;
import org.ohdsi.webapi.JobInvalidator;
import org.ohdsi.webapi.cohortcharacterization.converter.SerializedCcToCcConverter;
import org.ohdsi.webapi.cohortcharacterization.domain.CcFeAnalysisEntity;
import org.ohdsi.webapi.cohortcharacterization.domain.CcGenerationEntity;
import org.ohdsi.webapi.cohortcharacterization.domain.CcParamEntity;
import org.ohdsi.webapi.cohortcharacterization.domain.CcStrataConceptSetEntity;
import org.ohdsi.webapi.cohortcharacterization.domain.CcStrataEntity;
import org.ohdsi.webapi.cohortcharacterization.domain.CohortCharacterizationEntity;
import org.ohdsi.webapi.cohortcharacterization.dto.AbstractTemporalResult;
import org.ohdsi.webapi.cohortcharacterization.dto.CcDistributionStat;
import org.ohdsi.webapi.cohortcharacterization.dto.CcExportDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CcPrevalenceStat;
import org.ohdsi.webapi.cohortcharacterization.dto.CcResult;
import org.ohdsi.webapi.cohortcharacterization.dto.CcShortDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CcTemporalAnnualResult;
import org.ohdsi.webapi.cohortcharacterization.dto.CcTemporalResult;
import org.ohdsi.webapi.cohortcharacterization.dto.CcVersionFullDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.CohortCharacterizationDTO;
import org.ohdsi.webapi.cohortcharacterization.dto.ExecutionResultRequest;
import org.ohdsi.webapi.cohortcharacterization.dto.ExportExecutionResultRequest;
import org.ohdsi.webapi.cohortcharacterization.dto.GenerationResults;
import org.ohdsi.webapi.cohortcharacterization.report.AnalysisItem;
import org.ohdsi.webapi.cohortcharacterization.report.AnalysisResultItem;
import org.ohdsi.webapi.cohortcharacterization.report.ComparativeItem;
import org.ohdsi.webapi.cohortcharacterization.report.ExportItem;
import org.ohdsi.webapi.cohortcharacterization.report.PrevalenceItem;
import org.ohdsi.webapi.cohortcharacterization.report.Report;
import org.ohdsi.webapi.cohortcharacterization.report.TemporalAnnualItem;
import org.ohdsi.webapi.cohortcharacterization.report.TemporalItem;
import org.ohdsi.webapi.cohortcharacterization.repository.AnalysisGenerationInfoEntityRepository;
import org.ohdsi.webapi.cohortcharacterization.repository.CcConceptSetRepository;
import org.ohdsi.webapi.cohortcharacterization.repository.CcFeAnalysisRepository;
import org.ohdsi.webapi.cohortcharacterization.repository.CcGenerationEntityRepository;
import org.ohdsi.webapi.cohortcharacterization.repository.CcParamRepository;
import org.ohdsi.webapi.cohortcharacterization.repository.CcRepository;
import org.ohdsi.webapi.cohortcharacterization.repository.CcStrataRepository;
import org.ohdsi.webapi.cohortcharacterization.specification.CohortCharacterizationImpl;
import org.ohdsi.webapi.cohortdefinition.CohortDefinition;
import org.ohdsi.webapi.cohortdefinition.event.CohortDefinitionChangedEvent;
import org.ohdsi.webapi.common.DesignImportService;
import org.ohdsi.webapi.common.generation.AnalysisGenerationInfoEntity;
import org.ohdsi.webapi.common.generation.GenerationUtils;
import org.ohdsi.webapi.conceptset.ConceptSetExport;
import org.ohdsi.webapi.feanalysis.FeAnalysisService;
import org.ohdsi.webapi.feanalysis.domain.FeAnalysisCriteriaEntity;
import org.ohdsi.webapi.feanalysis.domain.FeAnalysisEntity;
import org.ohdsi.webapi.feanalysis.domain.FeAnalysisWithCriteriaEntity;
import org.ohdsi.webapi.feanalysis.domain.FeAnalysisWithStringEntity;
import org.ohdsi.webapi.feanalysis.event.FeAnalysisChangedEvent;
import org.ohdsi.webapi.job.GeneratesNotification;
import org.ohdsi.webapi.job.JobExecutionResource;
import org.ohdsi.webapi.service.AbstractDaoService;
import org.ohdsi.webapi.service.FeatureExtractionService;
import org.ohdsi.webapi.service.JobService;
import org.ohdsi.webapi.service.VocabularyService;
import org.ohdsi.webapi.shiro.Entities.UserEntity;
import org.ohdsi.webapi.shiro.annotations.CcGenerationId;
import org.ohdsi.webapi.shiro.annotations.DataSourceAccess;
import org.ohdsi.webapi.shiro.annotations.SourceKey;
import org.ohdsi.webapi.source.Source;
import org.ohdsi.webapi.source.SourceInfo;
import org.ohdsi.webapi.source.SourceService;
import org.ohdsi.webapi.sqlrender.SourceAwareSqlRender;
import org.ohdsi.webapi.tag.dto.TagNameListRequestDTO;
import org.ohdsi.webapi.util.CancelableJdbcTemplate;
import org.ohdsi.webapi.util.EntityUtils;
import org.ohdsi.webapi.util.ExceptionUtils;
import org.ohdsi.webapi.util.ExportUtil;
import org.ohdsi.webapi.util.NameUtils;
import org.ohdsi.webapi.util.SessionUtils;
import org.ohdsi.webapi.util.SourceUtils;
import org.ohdsi.webapi.util.TempFileUtils;
import org.ohdsi.webapi.versioning.domain.CharacterizationVersion;
import org.ohdsi.webapi.versioning.domain.Version;
import org.ohdsi.webapi.versioning.domain.VersionBase;
import org.ohdsi.webapi.versioning.domain.VersionType;
import org.ohdsi.webapi.versioning.dto.VersionDTO;
import org.ohdsi.webapi.versioning.dto.VersionUpdateDTO;
import org.ohdsi.webapi.versioning.service.VersionService;
import org.springframework.batch.core.BatchStatus;
import org.springframework.batch.core.JobExecution;
import org.springframework.batch.core.JobParameters;
import org.springframework.batch.core.JobParametersBuilder;
import org.springframework.batch.core.job.builder.SimpleJobBuilder;
import org.springframework.batch.core.repository.JobRepository;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.context.ApplicationEventPublisher;
import org.springframework.context.annotation.DependsOn;
import org.springframework.context.event.EventListener;
import org.springframework.core.convert.ConversionService;
import org.springframework.core.convert.support.GenericConversionService;
import org.springframework.core.env.Environment;
import org.springframework.data.domain.Page;
import org.springframework.data.domain.Pageable;
import org.springframework.jdbc.core.RowMapper;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import javax.annotation.PostConstruct;
import javax.persistence.EntityManager;
import javax.ws.rs.InternalServerErrorException;
import javax.ws.rs.NotFoundException;
import java.io.File;
import java.io.IOException;
import java.io.OutputStream;
import java.sql.ResultSet;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Objects;
import java.util.Optional;
import java.util.Set;
import java.util.function.BiConsumer;
import java.util.function.Consumer;
import java.util.function.Function;
import java.util.function.Predicate;
import java.util.function.Supplier;
import java.util.stream.Collectors;
import static java.util.stream.Collectors.groupingBy;
import static org.ohdsi.analysis.cohortcharacterization.design.CcResultType.DISTRIBUTION;
import static org.ohdsi.analysis.cohortcharacterization.design.CcResultType.PREVALENCE;
import static org.ohdsi.webapi.Constants.GENERATE_COHORT_CHARACTERIZATION;
import static org.ohdsi.webapi.Constants.Params.COHORT_CHARACTERIZATION_ID;
import static org.ohdsi.webapi.Constants.Params.JOB_AUTHOR;
import static org.ohdsi.webapi.Constants.Params.JOB_NAME;
import static org.ohdsi.webapi.Constants.Params.SOURCE_ID;
import org.ohdsi.webapi.security.PermissionService;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.data.domain.PageImpl;
@Service
@Transactional
@DependsOn({"ccExportDTOToCcEntityConverter", "cohortDTOToCohortDefinitionConverter", "feAnalysisDTOToFeAnalysisConverter"})
public class CcServiceImpl extends AbstractDaoService implements CcService, GeneratesNotification {
private static final String GENERATION_NOT_FOUND_ERROR = "generation cannot be found by id %d";
private static final String[] PARAMETERS_RESULTS = {"cohort_characterization_generation_id", "threshold_level", "vocabulary_schema"};
private static final String[] PARAMETERS_RESULTS_FILTERED = {"cohort_characterization_generation_id", "threshold_level",
"analysis_ids", "cohort_ids", "vocabulary_schema"};
private static final String[] PARAMETERS_COUNT = {"cohort_characterization_generation_id", "vocabulary_schema"};
private static final String[] PREVALENCE_STATS_PARAMS = {"cdm_database_schema", "cdm_results_schema", "cc_generation_id", "analysis_id", "cohort_id", "covariate_id"};
private final String QUERY_RESULTS = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/queryResults.sql");
private final String QUERY_TEMPORAL_RESULTS = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/queryTemporalResults.sql");
private final String QUERY_TEMPORAL_ANNUAL_RESULTS = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/queryTemporalAnnualResults.sql");
private final String QUERY_COUNT = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/queryCountWithoutThreshold.sql");
private final String DELETE_RESULTS = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/deleteResults.sql");
private final String DELETE_EXECUTION = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/deleteExecution.sql");
private final String QUERY_PREVALENCE_STATS = ResourceHelper.GetResourceAsString("/resources/cohortcharacterizations/sql/queryCovariateStatsVocab.sql");
private final String HYDRA_PACKAGE = "/resources/cohortcharacterizations/hydra/CohortCharacterization_v0.0.1.zip";
private final static List<String> INCOMPLETE_STATUSES = ImmutableList.of(BatchStatus.STARTED, BatchStatus.STARTING, BatchStatus.STOPPING, BatchStatus.UNKNOWN)
.stream().map(BatchStatus::name).collect(Collectors.toList());
private Map<String, FeatureExtraction.PrespecAnalysis> prespecAnalysisMap = FeatureExtraction.getNameToPrespecAnalysis();
private final EntityGraph defaultEntityGraph = EntityUtils.fromAttributePaths(
"cohortDefinitions",
"featureAnalyses",
"stratas",
"parameters",
"createdBy",
"modifiedBy"
);
private final List<String[]> executionPrevalenceHeaderLines = new ArrayList<String[]>() {{
add(new String[]{"Analysis ID", "Analysis name", "Strata ID",
"Strata name", "Cohort ID", "Cohort name", "Covariate ID", "Covariate name", "Covariate short name",
"Count", "Percent"});
}};
private final List<String[]> executionDistributionHeaderLines = new ArrayList<String[]>() {{
add(new String[]{"Analysis ID", "Analysis name", "Strata ID",
"Strata name", "Cohort ID", "Cohort name", "Covariate ID", "Covariate name", "Covariate short name", "Value field","Missing Means Zero",
"Count", "Avg", "StdDev", "Min", "P10", "P25", "Median", "P75", "P90", "Max"});
}};
private final List<String[]> executionComparativeHeaderLines = new ArrayList<String[]>() {{
add(new String[]{"Analysis ID", "Analysis name", "Strata ID",
"Strata name", "Target cohort ID", "Target cohort name", "Comparator cohort ID", "Comparator cohort name",
"Covariate ID", "Covariate name", "Covariate short name", "Target count", "Target percent",
"Comparator count", "Comparator percent", "Std. Diff Of Mean"});
}};
private final CcRepository repository;
private final CcParamRepository paramRepository;
private final CcStrataRepository strataRepository;
private final CcConceptSetRepository conceptSetRepository;
private final FeAnalysisService analysisService;
private final CcGenerationEntityRepository ccGenerationRepository;
private final FeatureExtractionService featureExtractionService;
private final DesignImportService designImportService;
private final AnalysisGenerationInfoEntityRepository analysisGenerationInfoEntityRepository;
private final SourceService sourceService;
private final GenerationUtils generationUtils;
private final EntityManager entityManager;
private final ApplicationEventPublisher eventPublisher;
private final JobRepository jobRepository;
private final SourceAwareSqlRender sourceAwareSqlRender;
private final JobService jobService;
private final JobInvalidator jobInvalidator;
private final GenericConversionService genericConversionService;
private final VocabularyService vocabularyService;
private final CcFeAnalysisRepository ccFeAnalysisRepository;
private VersionService<CharacterizationVersion> versionService;
private PermissionService permissionService;
@Value("${security.defaultGlobalReadPermissions}")
private boolean defaultGlobalReadPermissions;
private final Environment env;
public CcServiceImpl(
final CcRepository ccRepository,
final CcParamRepository paramRepository,
final CcStrataRepository strataRepository,
final CcConceptSetRepository conceptSetRepository,
final FeAnalysisService analysisService,
final CcGenerationEntityRepository ccGenerationRepository,
final FeatureExtractionService featureExtractionService,
final ConversionService conversionService,
final DesignImportService designImportService,
final JobRepository jobRepository,
final AnalysisGenerationInfoEntityRepository analysisGenerationInfoEntityRepository,
final SourceService sourceService,
final GenerationUtils generationUtils,
final SourceAwareSqlRender sourceAwareSqlRender,
final EntityManager entityManager,
final JobService jobService,
final ApplicationEventPublisher eventPublisher,
final JobInvalidator jobInvalidator,
final VocabularyService vocabularyService,
CcFeAnalysisRepository ccFeAnalysisRepository, final VersionService<CharacterizationVersion> versionService,
final PermissionService permissionService,
@Qualifier("conversionService") final GenericConversionService genericConversionService,
Environment env) {
this.repository = ccRepository;
this.paramRepository = paramRepository;
this.strataRepository = strataRepository;
this.conceptSetRepository = conceptSetRepository;
this.analysisService = analysisService;
this.ccGenerationRepository = ccGenerationRepository;
this.featureExtractionService = featureExtractionService;
this.designImportService = designImportService;
this.jobRepository = jobRepository;
this.analysisGenerationInfoEntityRepository = analysisGenerationInfoEntityRepository;
this.sourceService = sourceService;
this.generationUtils = generationUtils;
this.sourceAwareSqlRender = sourceAwareSqlRender;
this.entityManager = entityManager;
this.jobService = jobService;
this.eventPublisher = eventPublisher;
this.jobInvalidator = jobInvalidator;
this.vocabularyService = vocabularyService;
this.ccFeAnalysisRepository = ccFeAnalysisRepository;
this.permissionService = permissionService;
this.genericConversionService = genericConversionService;
this.versionService = versionService;
this.env = env;
SerializedCcToCcConverter.setConversionService(conversionService);
}
@Override
public CohortCharacterizationEntity createCc(final CohortCharacterizationEntity entity) {
entity.setCreatedBy(getCurrentUser());
entity.setCreatedDate(new Date());
return saveCc(entity);
}
private CohortCharacterizationEntity saveCc(final CohortCharacterizationEntity entity) {
CohortCharacterizationEntity savedEntity = repository.save(entity);
for(CcStrataEntity strata: entity.getStratas()){
strata.setCohortCharacterization(savedEntity);
strataRepository.save(strata);
}
for(CcParamEntity param: entity.getParameters()){
param.setCohortCharacterization(savedEntity);
paramRepository.save(param);
}
for(CcFeAnalysisEntity analysis : entity.getCcFeatureAnalyses()) {
analysis.setCohortCharacterization(savedEntity);
ccFeAnalysisRepository.save(analysis);
}
entityManager.flush();
entityManager.refresh(savedEntity);
savedEntity = findByIdWithLinkedEntities(savedEntity.getId());
Date modifiedDate = savedEntity.getModifiedDate();
savedEntity.setModifiedDate(null);
final String serialized = this.serializeCc(savedEntity);
savedEntity.setHashCode(serialized.hashCode());
savedEntity.setModifiedDate(modifiedDate);
return repository.save(savedEntity);
}
@EventListener
@Transactional
@Override
public void onCohortDefinitionChanged(CohortDefinitionChangedEvent event) {
List<CohortCharacterizationEntity> ccList = repository.findByCohortDefinition(event.getCohortDefinition());
ccList.forEach(this::saveCc);
}
@EventListener
@Transactional
public void onFeAnalysisChanged(FeAnalysisChangedEvent event) {
List<CohortCharacterizationEntity> ccList = repository.findByFeatureAnalysis(event.getFeAnalysis());
ccList.forEach(this::saveCc);
}
@Override
@Transactional
public void assignTag(Long id, int tagId) {
CohortCharacterizationEntity entity = findById(id);
assignTag(entity, tagId);
}
@Override
@Transactional
public void unassignTag(Long id, int tagId) {
CohortCharacterizationEntity entity = findById(id);
unassignTag(entity, tagId);
}
@Override
public int getCountCcWithSameName(Long id, String name) {
return repository.getCountCcWithSameName(id, name);
}
@Override
public void deleteCc(Long ccId) {
repository.delete(ccId);
}
@Override
public CohortCharacterizationEntity updateCc(final CohortCharacterizationEntity entity) {
final CohortCharacterizationEntity foundEntity = repository.findById(entity.getId())
.orElseThrow(() -> new NotFoundException("CC entity isn't found"));
updateLinkedFields(entity, foundEntity);
if (StringUtils.isNotEmpty(entity.getName())) {
foundEntity.setName(entity.getName());
}
foundEntity.setDescription(entity.getDescription());
foundEntity.setStratifiedBy(entity.getStratifiedBy());
if (Objects.nonNull(entity.getStrataOnly())) {
foundEntity.setStrataOnly(entity.getStrataOnly());
}
foundEntity.setModifiedDate(new Date());
foundEntity.setModifiedBy(getCurrentUser());
return saveCc(foundEntity);
}
private void updateLinkedFields(final CohortCharacterizationEntity entity, final CohortCharacterizationEntity foundEntity) {
updateConceptSet(entity, foundEntity);
updateParams(entity, foundEntity);
updateAnalyses(entity, foundEntity);
updateCohorts(entity, foundEntity);
updateStratas(entity, foundEntity);
}
private void updateConceptSet(CohortCharacterizationEntity entity, CohortCharacterizationEntity foundEntity) {
if (Objects.nonNull(foundEntity.getConceptSetEntity()) && Objects.nonNull(entity.getConceptSetEntity())) {
foundEntity.getConceptSetEntity().setRawExpression(entity.getConceptSetEntity().getRawExpression());
} else if (Objects.nonNull(entity.getConceptSetEntity())) {
CcStrataConceptSetEntity cse = new CcStrataConceptSetEntity();
cse.setCohortCharacterization(foundEntity);
cse.setRawExpression(entity.getConceptSetEntity().getRawExpression());
foundEntity.setConceptSetEntity(cse);
} else {
foundEntity.setConceptSetEntity(null);
}
}
private void updateStratas(CohortCharacterizationEntity entity, CohortCharacterizationEntity foundEntity) {
final List<CcStrataEntity> stratasToDelete = getLinksToDelete(foundEntity,
existingLink -> entity.getStratas().stream().noneMatch(newLink -> Objects.equals(newLink.getId(), existingLink.getId())),
CohortCharacterizationEntity::getStratas);
foundEntity.getStratas().removeAll(stratasToDelete);
strataRepository.delete(stratasToDelete);
Map<Long, CcStrataEntity> strataEntityMap = foundEntity.getStratas().stream()
.collect(Collectors.toMap(CcStrataEntity::getId, s -> s));
List<CcStrataEntity> updatedStratas = entity.getStratas().stream().map(updated -> {
updated.setCohortCharacterization(foundEntity);
if (Objects.nonNull(updated.getId())) {
CcStrataEntity strata = strataEntityMap.get(updated.getId());
// strata will be null in case of importing new characterization
if (strata == null) {
return updated;
}
if (StringUtils.isNotBlank(updated.getName())) {
strata.setName(updated.getName());
}
strata.setExpressionString(updated.getExpressionString());
return strata;
} else {
return updated;
}
}).collect(Collectors.toList());
entity.setStratas(new HashSet<>(strataRepository.save(updatedStratas)));
}
private void updateCohorts(final CohortCharacterizationEntity entity, final CohortCharacterizationEntity foundEntity) {
foundEntity.getCohortDefinitions().clear();
foundEntity.getCohortDefinitions().addAll(entity.getCohortDefinitions());
}
private void updateAnalyses(final CohortCharacterizationEntity entity, final CohortCharacterizationEntity foundEntity) {
ccFeAnalysisRepository.delete(foundEntity.getCcFeatureAnalyses());
foundEntity.getCcFeatureAnalyses().clear();
foundEntity.getCcFeatureAnalyses().addAll(entity.getCcFeatureAnalyses());
ccFeAnalysisRepository.save(foundEntity.getCcFeatureAnalyses());
}
private <T extends WithId> List<T> getLinksToDelete(final CohortCharacterizationEntity foundEntity,
Predicate<? super T> filterPredicate,
Function<CohortCharacterizationEntity, Set<T>> getter) {
return getter.apply(foundEntity)
.stream()
.filter(filterPredicate)
.collect(Collectors.toList());
}
private void updateParams(final CohortCharacterizationEntity entity, final CohortCharacterizationEntity foundEntity) {
updateOrCreateParams(entity, foundEntity);
deleteParams(entity, foundEntity);
}
private void deleteParams(final CohortCharacterizationEntity entity, final CohortCharacterizationEntity foundEntity) {
final Map<String, CcParamEntity> nameToParamFromInputMap = buildParamNameToParamMap(entity);
List<CcParamEntity> paramsForDelete = getLinksToDelete(foundEntity,
parameter -> !nameToParamFromInputMap.containsKey(parameter.getName()),
CohortCharacterizationEntity::getParameters);
foundEntity.getParameters().removeAll(paramsForDelete);
paramRepository.delete(paramsForDelete);
}
private void updateOrCreateParams(final CohortCharacterizationEntity entity, final CohortCharacterizationEntity foundEntity) {
final Map<String, CcParamEntity> nameToParamFromDbMap = buildParamNameToParamMap(foundEntity);
final List<CcParamEntity> paramsForCreateOrUpdate = new ArrayList<>();
for (final CcParamEntity parameter : entity.getParameters()) {
final CcParamEntity entityFromMap = nameToParamFromDbMap.get(parameter.getName());
parameter.setCohortCharacterization(foundEntity);
if (entityFromMap == null) {
paramsForCreateOrUpdate.add(parameter);
} else if (!StringUtils.equals(entityFromMap.getValue(), parameter.getValue())) {
entityFromMap.setValue(parameter.getValue());
paramsForCreateOrUpdate.add(entityFromMap);
}
}
paramRepository.save(paramsForCreateOrUpdate);
}
@Override
public CohortCharacterizationEntity importCc(final CohortCharacterizationEntity entity) {
cleanIds(entity);
final CohortCharacterizationEntity newCohortCharacterization = new CohortCharacterizationEntity();
newCohortCharacterization.setName(entity.getName());
final CohortCharacterizationEntity persistedCohortCharacterization = this.createCc(newCohortCharacterization);
updateParams(entity, persistedCohortCharacterization);
updateStratas(entity, persistedCohortCharacterization);
updateConceptSet(entity, persistedCohortCharacterization);
importCohorts(entity, persistedCohortCharacterization);
final CohortCharacterizationEntity savedEntity = saveCc(persistedCohortCharacterization);
List<Integer> savedAnalysesIds = importAnalyses(entity, savedEntity);
eventPublisher.publishEvent(new CcImportEvent(savedAnalysesIds));
return savedEntity;
}
@Override
public String getNameForCopy(String dtoName) {
return NameUtils.getNameForCopy(dtoName, this::getNamesLike, repository.findByName(dtoName));
}
@Override
public String getNameWithSuffix(String dtoName) {
return NameUtils.getNameWithSuffix(dtoName, this::getNamesLike);
}
@Override
public String serializeCc(final Long id) {
return Utils.serialize(exportCc(id), true);
}
@Override
public String serializeCc(final CohortCharacterizationEntity cohortCharacterizationEntity) {
return new SerializedCcToCcConverter().convertToDatabaseColumn(cohortCharacterizationEntity);
}
private CohortCharacterizationImpl exportCc(final Long id) {
final CohortCharacterizationEntity cohortCharacterizationEntity = repository.findById(id)
.orElseThrow(() -> new IllegalArgumentException("Cohort characterization cannot be found by id: " + id));
CohortCharacterizationImpl cc = genericConversionService.convert(cohortCharacterizationEntity, CohortCharacterizationImpl.class);
ExportUtil.clearCreateAndUpdateInfo(cc);
cc.getFeatureAnalyses().forEach(ExportUtil::clearCreateAndUpdateInfo);
cc.getCohorts().forEach(ExportUtil::clearCreateAndUpdateInfo);
cc.setOrganizationName(env.getRequiredProperty("organization.name"));
return cc;
}
@Override
public CohortCharacterizationEntity findById(final Long id) {
return repository.findById(id)
.orElseThrow(() -> new IllegalArgumentException("Cohort characterization with id: " + id + " cannot be found"));
}
@Override
public CohortCharacterizationEntity findByIdWithLinkedEntities(final Long id) {
return repository.findOne(id, defaultEntityGraph);
}
@Override
@DataSourceAccess
public CohortCharacterization findDesignByGenerationId(@CcGenerationId final Long id) {
final AnalysisGenerationInfoEntity entity = analysisGenerationInfoEntityRepository.findById(id)
.orElseThrow(() -> new IllegalArgumentException("Analysis with id: " + id + " cannot be found"));
return genericConversionService.convert(Utils.deserialize(entity.getDesign(),
new TypeReference<CcExportDTO>() {}), CohortCharacterizationEntity.class);
}
@Override
public Page<CohortCharacterizationEntity> getPageWithLinkedEntities(final Pageable pageable) {
return repository.findAll(pageable, defaultEntityGraph);
}
@Override
public Page<CohortCharacterizationEntity> getPage(final Pageable pageable) {
List<CohortCharacterizationEntity> ccList = repository.findAll()
.stream().filter(!defaultGlobalReadPermissions ? entity -> permissionService.hasReadAccess(entity) : entity -> true)
.collect(Collectors.toList());
return getPageFromResults(pageable, ccList);
}
private Page<CohortCharacterizationEntity> getPageFromResults(Pageable pageable, List<CohortCharacterizationEntity> results) {
// Calculate the start and end indices for the current page
int startIndex = pageable.getPageNumber() * pageable.getPageSize();
int endIndex = Math.min(startIndex + pageable.getPageSize(), results.size());
return new PageImpl<>(results.subList(startIndex, endIndex), pageable, results.size());
}
@Override
public void hydrateAnalysis(Long analysisId, String packageName, OutputStream out) {
if (packageName == null || !Utils.isAlphaNumeric(packageName)) {
throw new IllegalArgumentException("The package name must be alphanumeric only.");
}
CohortCharacterizationImpl analysis = exportCc(analysisId);
analysis.setPackageName(packageName);
String studySpecs = Utils.serialize(analysis, true);
Hydra hydra = new Hydra(studySpecs);
File skeletonFile = null;
try {
skeletonFile = TempFileUtils.copyResourceToTempFile(HYDRA_PACKAGE, "cc-", ".zip");
hydra.setExternalSkeletonFileName(skeletonFile.getAbsolutePath());
hydra.hydrate(out);
} catch (IOException e) {
log.error("Failed to hydrate cohort characterization", e);
throw new InternalServerErrorException(e);
} finally {
FileUtils.deleteQuietly(skeletonFile);
}
}
@Override
@DataSourceAccess
public JobExecutionResource generateCc(final Long id, @SourceKey final String sourceKey) {
CcService ccService = this;
Source source = getSourceRepository().findBySourceKey(sourceKey);
JobParametersBuilder builder = new JobParametersBuilder();
builder.addString(JOB_NAME, String.format("Generating cohort characterization %d : %s (%s)", id, source.getSourceName(), source.getSourceKey()));
builder.addString(COHORT_CHARACTERIZATION_ID, String.valueOf(id));
builder.addString(SOURCE_ID, String.valueOf(source.getSourceId()));
builder.addString(JOB_AUTHOR, getCurrentUserLogin());
CancelableJdbcTemplate jdbcTemplate = getSourceJdbcTemplate(source);
SimpleJobBuilder generateCohortJob = generationUtils.buildJobForCohortBasedAnalysisTasklet(
GENERATE_COHORT_CHARACTERIZATION,
source,
builder,
jdbcTemplate,
chunkContext -> {
Long ccId = Long.valueOf(chunkContext.getStepContext().getJobParameters().get(COHORT_CHARACTERIZATION_ID).toString());
return ccService.findById(ccId).getCohortDefinitions();
},
new GenerateCohortCharacterizationTasklet(
jdbcTemplate,
getTransactionTemplate(),
ccService,
analysisGenerationInfoEntityRepository,
sourceService,
userRepository
)
);
final JobParameters jobParameters = builder.toJobParameters();
return jobService.runJob(generateCohortJob.build(), jobParameters);
}
@Override
public List<CcGenerationEntity> findGenerationsByCcId(final Long id) {
return ccGenerationRepository.findByCohortCharacterizationIdOrderByIdDesc(id, EntityUtils.fromAttributePaths("source"));
}
@Override
public CcGenerationEntity findGenerationById(final Long id) {
return ccGenerationRepository.findById(id, EntityUtils.fromAttributePaths("source"));
}
@Override
public List<CcGenerationEntity> findGenerationsByCcIdAndSource(final Long id, final String sourceKey) {
return ccGenerationRepository.findByCohortCharacterizationIdAndSourceSourceKeyOrderByIdDesc(id, sourceKey, EntityUtils.fromAttributePaths("source"));
}
public List<CcGenerationEntity> findAllIncompleteGenerations() {
return ccGenerationRepository.findByStatusIn(INCOMPLETE_STATUSES);
}
protected List<CcResult> findResults(final Long generationId, ExecutionResultRequest params) {
return executeFindResults(generationId, params, QUERY_RESULTS, getGenerationResults());
}
private List<CcTemporalResult> findTemporalResults(final Long generationId, ExecutionResultRequest params) {
return executeFindResults(generationId, params, QUERY_TEMPORAL_RESULTS, getGenerationTemporalResult());
}
private List<CcTemporalAnnualResult> findTemporalAnnualResults(final Long generationId, ExecutionResultRequest params) {
return executeFindResults(generationId, params, QUERY_TEMPORAL_ANNUAL_RESULTS, getGenerationTemporalAnnualResult());
}
private <T> List<T> executeFindResults(final Long generationId, ExecutionResultRequest params, String query, RowMapper<T> rowMapper) {
final CcGenerationEntity generationEntity = ccGenerationRepository.findById(generationId)
.orElseThrow(() -> new IllegalArgumentException(String.format(GENERATION_NOT_FOUND_ERROR, generationId)));
final Source source = generationEntity.getSource();
String analysis = params.getAnalysisIds().stream().map(String::valueOf).collect(Collectors.joining(","));
String cohorts = params.getCohortIds().stream().map(String::valueOf).collect(Collectors.joining(","));
String generationResults = sourceAwareSqlRender.renderSql(source.getSourceId(), query, PARAMETERS_RESULTS_FILTERED,
new String[]{String.valueOf(generationId), String.valueOf(params.getThresholdValuePct()),
analysis, cohorts, SourceUtils.getVocabularyQualifier(source)});
final String tempSchema = SourceUtils.getTempQualifier(source);
String translatedSql = SqlTranslate.translateSql(generationResults, source.getSourceDialect(), SessionUtils.sessionId(), tempSchema);
return this.getSourceJdbcTemplate(source).query(translatedSql, rowMapper);
}
@Override
@DataSourceAccess
public Long getCCResultsTotalCount(@CcGenerationId final Long generationId) {
final CcGenerationEntity generationEntity = ccGenerationRepository.findById(generationId)
.orElseThrow(() -> new IllegalArgumentException(String.format(GENERATION_NOT_FOUND_ERROR, generationId)));
final Source source = generationEntity.getSource();
String countReq = sourceAwareSqlRender.renderSql(source.getSourceId(), QUERY_COUNT, PARAMETERS_COUNT,
new String[]{String.valueOf(generationId), SourceUtils.getVocabularyQualifier(source)});
final String tempSchema = SourceUtils.getTempQualifier(source);
String translatedSql = SqlTranslate.translateSql(countReq, source.getSourceDialect(), SessionUtils.sessionId(), tempSchema);
return this.getSourceJdbcTemplate(source).queryForObject(translatedSql, Long.class);
}
@Override
@DataSourceAccess
public GenerationResults exportExecutionResult(@CcGenerationId final Long generationId, ExportExecutionResultRequest params) {
GenerationResults res = findResult(generationId, params);
if (params.isFilterUsed()) {
res.setReports(res.getReports().stream()
.filter(r -> params.isComparative() == null || params.isComparative() == r.isComparative)
.filter(r -> params.isSummary() == null || params.isSummary() == r.isSummary)
.collect(Collectors.toList()));
}
return res;
}
@Override
@DataSourceAccess
public GenerationResults findData(@CcGenerationId final Long generationId, ExecutionResultRequest params) {
if (params.getShowEmptyResults()) {
params.setThresholdValuePct(Constants.DEFAULT_THRESHOLD); //Don't cut threshold results when all results requested
}
GenerationResults res = findResult(generationId, params);
boolean hasComparativeReports = res.getReports().stream()
.anyMatch(report -> report.isComparative);
if (hasComparativeReports) {
// if there're comparative reports - return only them as simple reports won't be shown on ui
res.setReports(res.getReports().stream()
.filter(report -> report.isComparative)
.collect(Collectors.toList()));
}
res.setPrevalenceThreshold(params.getThresholdValuePct());
return res;
}
@Override
@DataSourceAccess
public List<CcResult> findResultAsList(@CcGenerationId final Long generationId, float thresholdLevel) {
ExecutionResultRequest params = new ExecutionResultRequest();
CcGenerationEntity generationEntity = ccGenerationRepository.findById(generationId)
.orElseThrow(() -> new IllegalArgumentException(String.format(GENERATION_NOT_FOUND_ERROR, generationId)));
CohortCharacterizationEntity characterization = generationEntity.getCohortCharacterization();
params.setThresholdValuePct(thresholdLevel);
params.setCohortIds(characterization.getCohortDefinitions().stream()
.map(CohortDefinition::getId).collect(Collectors.toList()));
params.setAnalysisIds(characterization.getFeatureAnalyses().stream()
.map(this::mapFeatureAnalysisId).collect(Collectors.toList()));
params.setDomainIds(generationEntity.getCohortCharacterization().getFeatureAnalyses().stream()
.map(fa -> fa.getDomain().toString()).distinct().collect(Collectors.toList()));
return findResults(generationId, params);
}
@Override
@DataSourceAccess
public List<CcTemporalResult> findTemporalResultAsList(@CcGenerationId final Long generationId) {
ExecutionResultRequest params = getExecutionResultRequest(generationId);
return findTemporalResults(generationId, params);
}
@DataSourceAccess
public List<CcTemporalAnnualResult> findTemporalAnnualResultAsList(@CcGenerationId final Long generationId) {
ExecutionResultRequest params = getExecutionResultRequest(generationId);
return findTemporalAnnualResults(generationId, params);
}
private ExecutionResultRequest getExecutionResultRequest(Long generationId) {
ExecutionResultRequest params = new ExecutionResultRequest();
CcGenerationEntity generationEntity = ccGenerationRepository.findById(generationId)
.orElseThrow(() -> new IllegalArgumentException(String.format(GENERATION_NOT_FOUND_ERROR, generationId)));
CohortCharacterizationEntity characterization = generationEntity.getCohortCharacterization();
params.setCohortIds(characterization.getCohortDefinitions().stream()
.map(CohortDefinition::getId).collect(Collectors.toList()));
params.setAnalysisIds(characterization.getFeatureAnalyses().stream()
.map(this::mapFeatureAnalysisId).collect(Collectors.toList()));
params.setDomainIds(generationEntity.getCohortCharacterization().getFeatureAnalyses().stream()
.map(fa -> fa.getDomain().toString()).distinct().collect(Collectors.toList()));
return params;
}
@Override
@DataSourceAccess
public GenerationResults findResult(@CcGenerationId final Long generationId, ExecutionResultRequest params) {
CcGenerationEntity generationEntity = ccGenerationRepository.findById(generationId)
.orElseThrow(() -> new IllegalArgumentException(String.format(GENERATION_NOT_FOUND_ERROR, generationId)));
CohortCharacterizationEntity characterization = generationEntity.getCohortCharacterization();
Set<CohortDefinition> cohortDefs = characterization.getCohorts();
Set<FeAnalysisEntity> featureAnalyses = characterization.getFeatureAnalyses();
// if filter is not used then it must be initialized first
if (!params.isFilterUsed()) {
params.setCohortIds(characterization.getCohortDefinitions().stream()
.map(CohortDefinition::getId).collect(Collectors.toList()));
params.setAnalysisIds(featureAnalyses.stream().map(this::mapFeatureAnalysisId).collect(Collectors.toList()));
params.setDomainIds(generationEntity.getCohortCharacterization().getFeatureAnalyses().stream()
.map(fa -> fa.getDomain().toString()).distinct().collect(Collectors.toList()));
} else {
List<Integer> analysisIds = params.getAnalysisIds().stream().map(analysisId -> {
FeAnalysisEntity fe = featureAnalyses.stream()
.filter(fa -> Objects.equals(fa.getId(), analysisId))
.findFirst()
.orElseThrow(() -> new IllegalArgumentException(String.format("Feature with id=%s not found in analysis", analysisId)));
return mapFeatureAnalysisId(fe);
}).collect(Collectors.toList());
params.setAnalysisIds(analysisIds);
}
// remove domains which cannot be used as corresponding analyses are not selected
params.getDomainIds().removeIf(s ->
featureAnalyses.stream()
.noneMatch(fe -> fe.getDomain().toString().equals(s) && params.getAnalysisIds().contains(mapFeatureAnalysisId(fe))));
// remove analyses which cannot be used as corresponding domains are not selected
params.getAnalysisIds().removeIf(s ->
featureAnalyses.stream()
.noneMatch(fe -> mapFeatureAnalysisId(fe).equals(s) && params.getDomainIds().contains(fe.getDomain().toString())));
List<CcResult> ccResults = findResults(generationId, params);
List<CcTemporalResult> ccTemporalResults = findTemporalResults(generationId, params);
// create initial structure and fill with results
Map<Integer, AnalysisItem> analysisMap = new HashMap<>();
ccResults
.stream()
.peek(cc -> {
if (StandardFeatureAnalysisType.PRESET.toString().equals(cc.getFaType())) {
featureAnalyses.stream()
.filter(fa -> Objects.equals(fa.getDesign(), cc.getAnalysisName()))
.findFirst()
.ifPresent(v -> cc.setAnalysisId(v.getId()));
}
})
.forEach(ccResult -> {
if (ccResult instanceof CcPrevalenceStat) {
analysisMap.putIfAbsent(ccResult.getAnalysisId(), new AnalysisItem());
AnalysisItem analysisItem = analysisMap.get(ccResult.getAnalysisId());
analysisItem.setType(ccResult.getResultType());
analysisItem.setName(ccResult.getAnalysisName());
analysisItem.setFaType(ccResult.getFaType());
List<CcResult> results = analysisItem.getOrCreateCovariateItem(
((CcPrevalenceStat) ccResult).getCovariateId(), ccResult.getStrataId());
results.add(ccResult);
}
});
cohortDefs = cohortDefs
.stream()
.filter(def -> params.getCohortIds().contains(def.getId()))
.collect(Collectors.toSet());
//Temporal
Map<Integer, FeatureExtraction.PrespecAnalysis> prespecAnalysisIdMap = FeatureExtraction.getNameToPrespecAnalysis().values()
.stream().collect(Collectors.toMap(a -> a.analysisId, a -> a));
List<CcTemporalResult> temporalResult = findTemporalResultAsList(generationId);
List<CcTemporalResult> mappedResult = temporalResult.stream().map(tr -> mapTemporalResult(featureAnalyses, prespecAnalysisIdMap, tr, CcTemporalResult::new,
(source, target) -> {
target.setStartDay(source.getStartDay());
target.setEndDay(source.getEndDay());
target.setTimeId(source.getTimeId());
}))
.collect(Collectors.toList());
Map<Integer, Map<Integer, Map<Long, List<CcTemporalResult>>>> temporalByCohort = groupByResult(mappedResult);
List<CcTemporalAnnualResult> temporalAnnualResult = findTemporalAnnualResultAsList(generationId);
List<CcTemporalAnnualResult> mappedAnnualResult = temporalAnnualResult.stream().map(tr -> mapTemporalResult(featureAnalyses, prespecAnalysisIdMap, tr, CcTemporalAnnualResult::new,
(source, target) -> {
target.setYear(source.getYear());
}))
.collect(Collectors.toList());
Map<Integer, Map<Integer, Map<Long, List<CcTemporalAnnualResult>>>> annualByCohort = groupByResult(mappedAnnualResult);
List<Report> reports = prepareReportData(analysisMap, cohortDefs, featureAnalyses, params);
reports.forEach(r -> {
r.items.stream()
.filter(i -> Objects.equals(i.getFaType(), StandardFeatureAnalysisType.PRESET.toString()))
.filter(o -> !r.isComparative)
.map(this::toPrevalenceItem)
.forEach(item -> {
setTemporal(temporalByCohort, item, cov -> {
List<TemporalItem> temporalItems = cov.stream().map(temp -> {
TemporalItem ti = new TemporalItem();
ti.setAvg(temp.getAvg());
ti.setCount(temp.getCount());
ti.setStartDay(temp.getStartDay());
ti.setEndDay(temp.getEndDay());
return ti;
}).collect(Collectors.toList());
item.setTemporal(temporalItems);
});
setTemporal(annualByCohort, item, cov -> {
List<TemporalAnnualItem> temporalAnnualItems = cov.stream().map(temp -> {
TemporalAnnualItem tai = new TemporalAnnualItem();
tai.setYear(temp.getYear());
tai.setAvg(temp.getAvg());
tai.setCount(temp.getCount());
return tai;
}).collect(Collectors.toList());
item.setTemporalAnnual(temporalAnnualItems);
});
});
});
GenerationResults res = new GenerationResults();
res.setReports(reports);
res.setCount(ccResults.size());
return res;
}
private PrevalenceItem<?> toPrevalenceItem(ExportItem<?> exportItem){
return PrevalenceItem.class.cast(exportItem);
}
private static <T extends AbstractTemporalResult> void setTemporal(Map<Integer, Map<Integer, Map<Long, List<T>>>> temporalByCohort, PrevalenceItem item, Consumer<List<T>> setter) {
Optional.ofNullable(temporalByCohort.get(item.getCohortId()))
.flatMap(cr -> Optional.ofNullable(cr.get(item.getAnalysisId()))
.flatMap(ar -> Optional.ofNullable(ar.get(item.getCovariateId()))))
.ifPresent(setter);
}
private static <T extends AbstractTemporalResult> Map<Integer, Map<Integer, Map<Long, List<T>>>> groupByResult(List<T> mappedAnnualResult) {
return mappedAnnualResult.stream()
.collect(groupingBy(T::getCohortId, groupingBy(T::getAnalysisId, groupingBy(T::getCovariateId))));
}
private static <T extends AbstractTemporalResult> T mapTemporalResult(
Set<FeAnalysisEntity> featureAnalyses,
Map<Integer, FeatureExtraction.PrespecAnalysis> prespecAnalysisIdMap,
T source,
Supplier<T> constructor,
BiConsumer<T, T> initializer
) {
T result = constructor.get();
String analysisName = prespecAnalysisIdMap.get(source.getAnalysisId()).analysisName;
Integer analysisId = featureAnalyses.stream().filter(fa -> Objects.equals(fa.getRawDesign(), analysisName))
.findFirst()
.map(FeAnalysisEntity::getId)
.orElseThrow(() -> new IllegalArgumentException(String.format("Preset analysis [%s} is not mapped to feature", analysisName)));
result.setAnalysisId(analysisId);
result.setCovariateId(source.getCovariateId());
result.setAvg(source.getAvg());
result.setCount(source.getCount());
result.setAnalysisName(source.getAnalysisName());
result.setCovariateName(source.getCovariateName());
result.setStrataId(source.getStrataId());
result.setCohortId(source.getCohortId());
result.setStrataName(source.getStrataName());
result.setConceptId(source.getConceptId());
initializer.accept(source, result);
return result;
}
private Integer mapFeatureAnalysisId(FeAnalysisEntity feAnalysis) {
if (feAnalysis.isPreset()) {
return prespecAnalysisMap.values().stream().filter(p -> Objects.equals(p.analysisName, feAnalysis.getDesign()))
.findFirst()
.orElseThrow(() -> new IllegalArgumentException(String.format("Preset analysis with id=%s does not exist", feAnalysis.getId())))
.analysisId;
} else {
return feAnalysis.getId();
}
}
private String mapFeatureName(FeAnalysisEntity entity) {
if (StandardFeatureAnalysisType.PRESET == entity.getType()) {
return entity.getDesign().toString();
}
return entity.getName();
}
private List<Report> prepareReportData(Map<Integer, AnalysisItem> analysisMap, Set<CohortDefinition> cohortDefs,
Set<FeAnalysisEntity> featureAnalyses, ExecutionResultRequest params) {
// Create map to get cohort name by its id
final Map<Integer, CohortDefinition> definitionMap = cohortDefs.stream()
.collect(Collectors.toMap(CohortDefinition::getId, Function.identity()));
// Create map to get feature analyses by its name
final Map<String, String> feAnalysisMap = featureAnalyses.stream()
.collect(Collectors.toMap(this::mapFeatureName, entity -> entity.getDomain().toString()));
List<Report> reports = new ArrayList<>();
try {
// list to accumulate results from simple reports
List<AnalysisResultItem> simpleResultSummary = new ArrayList<>();
// list to accumulate results from comparative reports
List<AnalysisResultItem> comparativeResultSummary = new ArrayList<>();
// do not create summary reports when only one analyses is present
boolean ignoreSummary = analysisMap.keySet().size() == 1;
for (Integer analysisId : analysisMap.keySet()) {
analysisMap.putIfAbsent(analysisId, new AnalysisItem());
AnalysisItem analysisItem = analysisMap.get(analysisId);
AnalysisResultItem resultItem = analysisItem.getSimpleItems(definitionMap, feAnalysisMap);
Report simpleReport = new Report(analysisItem.getName(), analysisId, resultItem);
simpleReport.faType = analysisItem.getFaType();
simpleReport.domainId = feAnalysisMap.get(analysisItem.getName());