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KarnaiahPesulaKarnaiahPesula
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AST format issue fixed.
Some minor issues fixed.
1 parent 3239a4c commit 31c75d0

10 files changed

Lines changed: 173 additions & 28 deletions

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‎sormas-api/src/main/java/de/symeda/sormas/api/exposure/ExposureDto.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -469,6 +469,7 @@ public class ExposureDto extends PseudonymizableDto {
469469

470470
@Diseases({
471471
Disease.SHIGELLOSIS })
472+
@SensitiveData
472473
private SexualContact sexualContact;
473474

474475
public static ExposureDto build(ExposureType exposureType) {

‎sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenSpecie.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -203,7 +203,7 @@ public enum PathogenSpecie {
203203
PathogenTestType.SEROGROUPING,
204204
PathogenTestType.SEROTYPING,
205205
PathogenTestType.BACTERIAL_CULTURE })
206-
SHISPP,
206+
SHIGELLA_SPP,
207207
@Diseases({
208208
Disease.MALARIA,
209209
Disease.SHIGELLOSIS })

‎sormas-api/src/main/java/de/symeda/sormas/api/sample/SerotypingMethod.java‎

Lines changed: 3 additions & 9 deletions
Original file line numberDiff line numberDiff line change
@@ -62,21 +62,15 @@ public enum SerotypingMethod {
6262
PathogenTestType.SEROGROUPING })
6363
SLIDE_AGGLUTINATION,
6464
@Diseases(value = {
65-
Disease.INVASIVE_PNEUMOCOCCAL_INFECTION,
66-
Disease.SHIGELLOSIS })
65+
Disease.INVASIVE_PNEUMOCOCCAL_INFECTION })
6766
@ApplicableToPathogenTests(value = {
6867
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
6968
DISK_DIFFUSION,
69+
7070
@Diseases(value = {
7171
Disease.SHIGELLOSIS })
7272
@ApplicableToPathogenTests(value = {
73-
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
74-
MIC_DETERMINATION,
75-
@Diseases(value = {
76-
Disease.SHIGELLOSIS })
77-
@ApplicableToPathogenTests(value = {
78-
PathogenTestType.SEROTYPING,
79-
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
73+
PathogenTestType.SEROTYPING })
8074
WGS_PREDICTION,
8175
// OTHER is mostly applicable for all diseases and pathogen tests, so we don't specify them as applicable to specific diseases or tests
8276
@Diseases

‎sormas-api/src/main/java/de/symeda/sormas/api/therapy/DrugSusceptibilityDto.java‎

Lines changed: 74 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -122,14 +122,19 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
122122

123123
public static final String AZITHROMYCIN_MIC = "azithromycinMic";
124124
public static final String AZITHROMYCIN_SUSCEPTIBILITY = "azithromycinSusceptibility";
125+
public static final String AZITHROMYCIN_METHOD = "azithromycinMethod";
125126
public static final String CEFTAZIDIME_MIC = "ceftazidimeMic";
126127
public static final String CEFTAZIDIME_SUSCEPTIBILITY = "ceftazidimeSusceptibility";
128+
public static final String CEFTAZIDIME_METHOD = "ceftazidimeMethod";
127129
public static final String CEFOTAXIME_MIC = "cefotaximeMic";
128130
public static final String CEFOTAXIME_SUSCEPTIBILITY = "cefotaximeSusceptibility";
131+
public static final String CEFOTAXIME_METHOD = "cefotaximeMethod";
129132
public static final String AMPICILLIN_MIC = "ampicillinMic";
130133
public static final String AMPICILLIN_SUSCEPTIBILITY = "ampicillinSusceptibility";
134+
public static final String AMPICILLIN_METHOD = "ampicillinMethod";
131135
public static final String TRIMETHOPRIM_SULFAMETHOXAZOLE_MIC = "trimethoprimSulfamethoxazoleMic";
132136
public static final String TRIMETHOPRIM_SULFAMETHOXAZOLE_SUSCEPTIBILITY = "trimethoprimSulfamethoxazoleSusceptibility";
137+
public static final String TRIMETHOPRIM_SULFAMETHOXAZOLE_METHOD = "trimethoprimSulfamethoxazoleMethod";
133138

134139
@Diseases(value = {
135140
Disease.TUBERCULOSIS })
@@ -364,7 +369,8 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
364369
private SusceptibilitySurveillanceType capreomycinSurveillance;
365370
@Diseases(value = {
366371
Disease.TUBERCULOSIS,
367-
Disease.INVASIVE_MENINGOCOCCAL_INFECTION })
372+
Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
373+
Disease.SHIGELLOSIS })
368374
@ApplicableToPathogenTests(value = {
369375
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
370376
private SusceptibilityMethod ciprofloxacinMethod;
@@ -535,7 +541,8 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
535541
private SusceptibilitySurveillanceType streptomycinSurveillance;
536542
@Diseases(value = {
537543
Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
538-
Disease.INVASIVE_PNEUMOCOCCAL_INFECTION })
544+
Disease.INVASIVE_PNEUMOCOCCAL_INFECTION,
545+
Disease.SHIGELLOSIS })
539546
@ApplicableToPathogenTests(value = {
540547
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
541548
private SusceptibilityMethod ceftriaxoneMethod;
@@ -595,6 +602,11 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
595602
@ApplicableToPathogenTests(value = {
596603
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
597604
private DrugSusceptibilityType azithromycinSusceptibility;
605+
@Diseases(value = {
606+
Disease.SHIGELLOSIS })
607+
@ApplicableToPathogenTests(value = {
608+
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
609+
private SusceptibilityMethod azithromycinMethod;
598610
@Diseases(value = {
599611
Disease.SHIGELLOSIS })
600612
@ApplicableToPathogenTests(value = {
@@ -606,6 +618,12 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
606618
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
607619
private DrugSusceptibilityType ceftazidimeSusceptibility;
608620

621+
@Diseases(value = {
622+
Disease.SHIGELLOSIS })
623+
@ApplicableToPathogenTests(value = {
624+
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
625+
private SusceptibilityMethod ceftazidimeMethod;
626+
609627
@Diseases(value = {
610628
Disease.SHIGELLOSIS })
611629
@ApplicableToPathogenTests(value = {
@@ -616,6 +634,11 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
616634
@ApplicableToPathogenTests(value = {
617635
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
618636
private DrugSusceptibilityType cefotaximeSusceptibility;
637+
@Diseases(value = {
638+
Disease.SHIGELLOSIS })
639+
@ApplicableToPathogenTests(value = {
640+
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
641+
private SusceptibilityMethod cefotaximeMethod;
619642
@Diseases(value = {
620643
Disease.SHIGELLOSIS })
621644
@ApplicableToPathogenTests(value = {
@@ -626,6 +649,11 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
626649
@ApplicableToPathogenTests(value = {
627650
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
628651
private DrugSusceptibilityType ampicillinSusceptibility;
652+
@Diseases(value = {
653+
Disease.SHIGELLOSIS })
654+
@ApplicableToPathogenTests(value = {
655+
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
656+
private SusceptibilityMethod ampicillinMethod;
629657
@Diseases(value = {
630658
Disease.SHIGELLOSIS })
631659
@ApplicableToPathogenTests(value = {
@@ -636,6 +664,11 @@ public class DrugSusceptibilityDto extends PseudonymizableDto {
636664
@ApplicableToPathogenTests(value = {
637665
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
638666
private DrugSusceptibilityType trimethoprimSulfamethoxazoleSusceptibility;
667+
@Diseases(value = {
668+
Disease.SHIGELLOSIS })
669+
@ApplicableToPathogenTests(value = {
670+
PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY })
671+
private SusceptibilityMethod trimethoprimSulfamethoxazoleMethod;
639672

640673
public static DrugSusceptibilityDto build() {
641674
DrugSusceptibilityDto drugSusceptibility = new DrugSusceptibilityDto();
@@ -1403,4 +1436,43 @@ public void setTrimethoprimSulfamethoxazoleSusceptibility(DrugSusceptibilityType
14031436
this.trimethoprimSulfamethoxazoleSusceptibility = trimethoprimSulfamethoxazoleSusceptibility;
14041437
}
14051438

1439+
public SusceptibilityMethod getAzithromycinMethod() {
1440+
return azithromycinMethod;
1441+
}
1442+
1443+
public void setAzithromycinMethod(SusceptibilityMethod azithromycinMethod) {
1444+
this.azithromycinMethod = azithromycinMethod;
1445+
}
1446+
1447+
public SusceptibilityMethod getCeftazidimeMethod() {
1448+
return ceftazidimeMethod;
1449+
}
1450+
1451+
public void setCeftazidimeMethod(SusceptibilityMethod ceftazidimeMethod) {
1452+
this.ceftazidimeMethod = ceftazidimeMethod;
1453+
}
1454+
1455+
public SusceptibilityMethod getCefotaximeMethod() {
1456+
return cefotaximeMethod;
1457+
}
1458+
1459+
public void setCefotaximeMethod(SusceptibilityMethod cefotaximeMethod) {
1460+
this.cefotaximeMethod = cefotaximeMethod;
1461+
}
1462+
1463+
public SusceptibilityMethod getAmpicillinMethod() {
1464+
return ampicillinMethod;
1465+
}
1466+
1467+
public void setAmpicillinMethod(SusceptibilityMethod ampicillinMethod) {
1468+
this.ampicillinMethod = ampicillinMethod;
1469+
}
1470+
1471+
public SusceptibilityMethod getTrimethoprimSulfamethoxazoleMethod() {
1472+
return trimethoprimSulfamethoxazoleMethod;
1473+
}
1474+
1475+
public void setTrimethoprimSulfamethoxazoleMethod(SusceptibilityMethod trimethoprimSulfamethoxazoleMethod) {
1476+
this.trimethoprimSulfamethoxazoleMethod = trimethoprimSulfamethoxazoleMethod;
1477+
}
14061478
}

‎sormas-api/src/main/resources/enum.properties‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1332,7 +1332,7 @@ PathogenSpecie.BOYDII=Shigella boydii
13321332
PathogenSpecie.DYSENTERIAE=Shigella dysenteriae
13331333
PathogenSpecie.FLEXNERI=Shigella flexneri
13341334
PathogenSpecie.SONNEI=Shigella sonnei
1335-
PathogenSpecie.SHISPP=Shigella spp
1335+
PathogenSpecie.SHIGELLA_SPP=Shigella spp
13361336
PathogenSpecie.NOT_SPECIFIED = Plasmodium species not specified
13371337
PathogenSpecie.COINFECTION = Plasmodium coinfection
13381338
PathogenSpecie.OTHER = Other
@@ -1553,7 +1553,6 @@ SerotypingMethod.GEL_DIFFUSION=Gel Diffusion
15531553
SerotypingMethod.PNEUMOTEST=Pneumotest
15541554
SerotypingMethod.SLIDE_AGGLUTINATION=Slide Agglutination
15551555
SerotypingMethod.DISK_DIFFUSION=Disk Diffusion
1556-
SerotypingMethod.MIC_DETERMINATION=MIC determination (E-test, broth microdilution)
15571556
SerotypingMethod.WGS_PREDICTION=WGS-based prediction
15581557
SerotypingMethod.OTHER=Other
15591558

‎sormas-backend/src/main/java/de/symeda/sormas/backend/therapy/DrugSusceptibility.java‎

Lines changed: 53 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -209,14 +209,23 @@ public class DrugSusceptibility extends AbstractDomainObject {
209209

210210
private Float azithromycinMic;
211211
private DrugSusceptibilityType azithromycinSusceptibility;
212+
213+
private SusceptibilityMethod azithromycinMethod;
214+
212215
private Float ceftazidimeMic;
213216
private DrugSusceptibilityType ceftazidimeSusceptibility;
217+
private SusceptibilityMethod ceftazidimeMethod;
218+
214219
private Float cefotaximeMic;
215220
private DrugSusceptibilityType cefotaximeSusceptibility;
221+
private SusceptibilityMethod cefotaximeMethod;
222+
216223
private Float ampicillinMic;
217224
private DrugSusceptibilityType ampicillinSusceptibility;
225+
private SusceptibilityMethod ampicillinMethod;
218226
private Float trimethoprimSulfamethoxazoleMic;
219227
private DrugSusceptibilityType trimethoprimSulfamethoxazoleSusceptibility;
228+
private SusceptibilityMethod trimethoprimSulfamethoxazoleMethod;
220229

221230
public Float getAmikacinMic() {
222231
return amikacinMic;
@@ -1034,4 +1043,48 @@ public void setTrimethoprimSulfamethoxazoleSusceptibility(DrugSusceptibilityType
10341043
this.trimethoprimSulfamethoxazoleSusceptibility = trimethoprimSulfamethoxazoleSusceptibility;
10351044
}
10361045

1046+
@Enumerated(EnumType.STRING)
1047+
public SusceptibilityMethod getAzithromycinMethod() {
1048+
return azithromycinMethod;
1049+
}
1050+
1051+
public void setAzithromycinMethod(SusceptibilityMethod azithromycinMethod) {
1052+
this.azithromycinMethod = azithromycinMethod;
1053+
}
1054+
1055+
@Enumerated(EnumType.STRING)
1056+
public SusceptibilityMethod getCeftazidimeMethod() {
1057+
return ceftazidimeMethod;
1058+
}
1059+
1060+
public void setCeftazidimeMethod(SusceptibilityMethod ceftazidimeMethod) {
1061+
this.ceftazidimeMethod = ceftazidimeMethod;
1062+
}
1063+
1064+
@Enumerated(EnumType.STRING)
1065+
public SusceptibilityMethod getCefotaximeMethod() {
1066+
return cefotaximeMethod;
1067+
}
1068+
1069+
public void setCefotaximeMethod(SusceptibilityMethod cefotaximeMethod) {
1070+
this.cefotaximeMethod = cefotaximeMethod;
1071+
}
1072+
1073+
@Enumerated(EnumType.STRING)
1074+
public SusceptibilityMethod getAmpicillinMethod() {
1075+
return ampicillinMethod;
1076+
}
1077+
1078+
public void setAmpicillinMethod(SusceptibilityMethod ampicillinMethod) {
1079+
this.ampicillinMethod = ampicillinMethod;
1080+
}
1081+
1082+
@Enumerated(EnumType.STRING)
1083+
public SusceptibilityMethod getTrimethoprimSulfamethoxazoleMethod() {
1084+
return trimethoprimSulfamethoxazoleMethod;
1085+
}
1086+
1087+
public void setTrimethoprimSulfamethoxazoleMethod(SusceptibilityMethod trimethoprimSulfamethoxazoleMethod) {
1088+
this.trimethoprimSulfamethoxazoleMethod = trimethoprimSulfamethoxazoleMethod;
1089+
}
10371090
}

‎sormas-backend/src/main/java/de/symeda/sormas/backend/therapy/DrugSusceptibilityMapper.java‎

Lines changed: 10 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -130,6 +130,11 @@ public static DrugSusceptibilityDto toDto(DrugSusceptibility source) {
130130
target.setAmpicillinSusceptibility(source.getAmpicillinSusceptibility());
131131
target.setTrimethoprimSulfamethoxazoleMic(source.getTrimethoprimSulfamethoxazoleMic());
132132
target.setTrimethoprimSulfamethoxazoleSusceptibility(source.getTrimethoprimSulfamethoxazoleSusceptibility());
133+
target.setAzithromycinMethod(source.getAzithromycinMethod());
134+
target.setAmpicillinMethod(source.getAmpicillinMethod());
135+
target.setCeftazidimeMethod(source.getCeftazidimeMethod());
136+
target.setCefotaximeMethod(source.getCefotaximeMethod());
137+
target.setTrimethoprimSulfamethoxazoleMethod(source.getTrimethoprimSulfamethoxazoleMethod());
133138

134139
return target;
135140
}
@@ -236,6 +241,11 @@ public DrugSusceptibility fillOrBuildEntity(@NotNull DrugSusceptibilityDto sourc
236241
target.setAmpicillinSusceptibility(source.getAmpicillinSusceptibility());
237242
target.setTrimethoprimSulfamethoxazoleMic(source.getTrimethoprimSulfamethoxazoleMic());
238243
target.setTrimethoprimSulfamethoxazoleSusceptibility(source.getTrimethoprimSulfamethoxazoleSusceptibility());
244+
target.setAzithromycinMethod(source.getAzithromycinMethod());
245+
target.setAmpicillinMethod(source.getAmpicillinMethod());
246+
target.setCeftazidimeMethod(source.getCeftazidimeMethod());
247+
target.setCefotaximeMethod(source.getCefotaximeMethod());
248+
target.setTrimethoprimSulfamethoxazoleMethod(source.getTrimethoprimSulfamethoxazoleMethod());
239249

240250
return target;
241251
}

‎sormas-backend/src/main/resources/sql/sormas_schema.sql‎

Lines changed: 13 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -16298,22 +16298,32 @@ INSERT INTO schema_version (version_number, comment) VALUES (637, 'Reference lab
1629816298
-- 04-06-2026 Shigellosis lab message processing. #13965
1629916299
ALTER TABLE testreport ADD COLUMN IF NOT EXISTS pathogentestcategory varchar(255);
1630016300
ALTER TABLE exposures ADD COLUMN IF NOT EXISTS sexualcontact varchar(255);
16301-
16301+
ALTER TABLE drugsusceptibility ADD COLUMN IF NOT EXISTS trimethoprimSulfamethoxazoleMethod varchar(255);
16302+
ALTER TABLE drugsusceptibility ADD COLUMN IF NOT EXISTS azithromycinMethod varchar(255);
16303+
ALTER TABLE drugsusceptibility ADD COLUMN IF NOT EXISTS ampicillinMethod varchar(255);
16304+
ALTER TABLE drugsusceptibility ADD COLUMN IF NOT EXISTS ceftazidimeMethod varchar(255);
16305+
ALTER TABLE drugsusceptibility ADD COLUMN IF NOT EXISTS cefotaximeMethod varchar(255);
1630216306

1630316307
DO $$
1630416308
BEGIN
1630516309
IF EXISTS (SELECT 1 FROM information_schema.columns WHERE table_schema = current_schema() AND table_name = 'healthconditions' AND column_name = 'undermedication')
16306-
AND NOT EXISTS (SELECT 1 FROM information_schema.columns WHERE table_schema = current_schema() AND table_name = 'healthconditions' AND column_name = 'undermedication') THEN
16310+
AND NOT EXISTS (SELECT 1 FROM information_schema.columns WHERE table_schema = current_schema() AND table_name = 'healthconditions' AND column_name = 'onmedication') THEN
1630716311
ALTER TABLE healthconditions RENAME COLUMN undermedication TO onmedication;
1630816312
END IF;
1630916313
IF EXISTS (SELECT 1 FROM information_schema.columns WHERE table_schema = current_schema() AND table_name = 'healthconditions' AND column_name = 'undermedication')
16310-
AND NOT EXISTS (SELECT 1 FROM information_schema.columns WHERE table_schema = current_schema() AND table_name = 'healthconditions' AND column_name = 'undermedication') THEN
16314+
AND NOT EXISTS (SELECT 1 FROM information_schema.columns WHERE table_schema = current_schema() AND table_name = 'healthconditions' AND column_name = 'onmedication') THEN
1631116315
ALTER TABLE healthconditions RENAME COLUMN undermedication TO onmedication;
1631216316
END IF;
1631316317
END $$;
1631416318

1631516319
ALTER TABLE testreport_history ADD COLUMN IF NOT EXISTS pathogentestcategory varchar(255);
1631616320
ALTER TABLE exposures_history ADD COLUMN IF NOT EXISTS sexualcontact varchar(255);
16321+
ALTER TABLE drugsusceptibility_history ADD COLUMN IF NOT EXISTS trimethoprimSulfamethoxazoleMethod varchar(255);
16322+
ALTER TABLE drugsusceptibility_history ADD COLUMN IF NOT EXISTS azithromycinMethod varchar(255);
16323+
ALTER TABLE drugsusceptibility_history ADD COLUMN IF NOT EXISTS ampicillinMethod varchar(255);
16324+
ALTER TABLE drugsusceptibility_history ADD COLUMN IF NOT EXISTS ceftazidimeMethod varchar(255);
16325+
ALTER TABLE drugsusceptibility_history ADD COLUMN IF NOT EXISTS cefotaximeMethod varchar(255);
16326+
1631716327

1631816328
DO $$
1631916329
BEGIN

‎sormas-ui/src/main/java/de/symeda/sormas/ui/samples/diseasesection/ShigellosisSectionComponent.java‎

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -156,16 +156,17 @@ private void updateFieldVisibility() {
156156
// SEROtype : test method + species + serotype:
157157
boolean showDrugSusceptibilityForm = currentTestType != null && currentTestType == PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY;
158158

159-
if (!isSerogrouping) {
160-
setVisibleClear(specie, serotypeTF, serotypingMethodCBF);
159+
if (!isSerogrouping && !isSerotype) {
160+
setVisibleClear(specie, specieTextField);
161161
}
162162
if (!isSerotype) {
163-
setVisibleClear(specieTextField, specie, serotypingMethodCBF, serotypeTF);
163+
setVisibleClear(serotypeTF);
164164
}
165-
if (!showDrugSusceptibilityForm) {
166-
setVisibleClear(serotypingMethodCBF);
165+
if (!isSerotype && !showDrugSusceptibilityForm) {
166+
setVisibleClear(serotypingMethodCBF, serotypingMethodTF);
167167
}
168-
serotypingMethodCBF.setVisible(isSerotype || showDrugSusceptibilityForm);
168+
169+
serotypingMethodCBF.setVisible(isSerotype);
169170
specie.setVisible(isSerotype || isSerogrouping);
170171
serotypeTF.setVisible(isSerotype);
171172
updateRowAndSelfVisibility();

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