Merge pull request #13643 from SORMAS-Foundation/13395-no-sanity-check-on-date-sample-was-sent

KarnaiahPesula · web-flow · commit a86feee59a98 · 2025-11-10T09:58:52.000+01:00
Defect fixes
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/Disease.java b/sormas-api/src/main/java/de/symeda/sormas/api/Disease.java
@@ -75,7 +75,7 @@ public enum Disease
 	INFLUENZA_B(false, true, true, false, false, 0, true, false, false),
 	H_METAPNEUMOVIRUS(true, false, true, false, false, 0, true, false, false),
 	RESPIRATORY_SYNCYTIAL_VIRUS(true, false, true, false, false, 0, true, false, false),
-	PARAINFLUENZA_1_4(true, false, true, false, false, 0, true, false, false),
+	PARAINFLUENZA_1_4(false, false, true, false, false, 0, true, false, false),
 	ADENOVIRUS(true, false, true, false, false, 0, true, false, false),
 	RHINOVIRUS(true, false, true, false, false, 0, true, false, false),
 	ENTEROVIRUS(true, false, true, false, false, 0, true, false, false),
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java b/sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java
@@ -2275,6 +2275,8 @@ public interface Captions {
 	String PathogenTest_prescriberPostalCode = "PathogenTest.prescriberPostalCode";
 	String PathogenTest_reportDate = "PathogenTest.reportDate";
 	String PathogenTest_rifampicinResistant = "PathogenTest.rifampicinResistant";
+	String PathogenTest_rsv_testedDiseaseVariant = "PathogenTest.rsv.testedDiseaseVariant";
+	String PathogenTest_rsv_testedDiseaseVariantDetails = "PathogenTest.rsv.testedDiseaseVariantDetails";
 	String PathogenTest_seroGroupSpecification = "PathogenTest.seroGroupSpecification";
 	String PathogenTest_seroGroupSpecificationText = "PathogenTest.seroGroupSpecificationText";
 	String PathogenTest_serotype = "PathogenTest.serotype";
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestType.java b/sormas-api/src/main/java/de/symeda/sormas/api/sample/PathogenTestType.java
@@ -161,7 +161,9 @@ public enum PathogenTestType {
 
 	@Diseases(value = {
 		Disease.RESPIRATORY_SYNCYTIAL_VIRUS,
-		Disease.MEASLES })
+		Disease.MEASLES,
+		Disease.INVASIVE_PNEUMOCOCCAL_INFECTION,
+		Disease.INVASIVE_MENINGOCOCCAL_INFECTION })
 	SEQUENCING,
 
 	@Diseases(value = {
diff --git a/sormas-api/src/main/java/de/symeda/sormas/api/symptoms/SymptomsDto.java b/sormas-api/src/main/java/de/symeda/sormas/api/symptoms/SymptomsDto.java
@@ -2525,7 +2525,8 @@ public static SymptomsDto build() {
 		UNDEFINED,
 		OTHER })
 	@HideForCountriesExcept(countries = {
-		CountryHelper.COUNTRY_CODE_SWITZERLAND })
+		CountryHelper.COUNTRY_CODE_SWITZERLAND,
+		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	@SymptomGrouping(SymptomGroup.GENERAL)
 	private SymptomState fatigue;
 	@Diseases({
diff --git a/sormas-api/src/main/resources/captions.properties b/sormas-api/src/main/resources/captions.properties
@@ -1149,7 +1149,7 @@ EpiData.caseImportedStatus=Case imported status
 EpiData.clusterRelated=Cluster Related
 EpiData.clusterType=Cluster type
 EpiData.clusterTypeText=Specify cluster type text
-EpiData.modeOfTransmission=Mode of transmission
+EpiData.modeOfTransmission=Suspected main mode of transmission
 EpiData.modeOfTransmissionType= Specify mode of transmission
 EpiData.infectionSource= Suspected vehicle or source of infection
 EpiData.infectionSourceText= Specify source of infection
@@ -1872,6 +1872,7 @@ PathogenTest.pcrTestSpecification=PCR/RT-PCR test specification
 PathogenTest.testTypeText=Specify test details
 PathogenTest.testedDisease=Tested disease
 PathogenTest.testedDiseaseVariant=Tested disease variant
+PathogenTest.rsv.testedDiseaseVariant=Tested disease subtype
 PathogenTest.testedDiseaseDetails=Tested disease name
 PathogenTest.testedPathogen=Tested pathogen
 PathogenTest.testedPathogenDetails=Tested pathogen details
@@ -1884,6 +1885,7 @@ PathogenTest.externalId=External ID
 PathogenTest.reportDate=Report date
 PathogenTest.viaLims=Via LIMS
 PathogenTest.testedDiseaseVariantDetails=Disease variant details
+PathogenTest.rsv.testedDiseaseVariantDetails=Disease subtype details
 PathogenTest.externalOrderId=External order ID
 PathogenTest.preliminary=Preliminary
 PathogenTest.ctValueE=Ct target E
diff --git a/sormas-api/src/main/resources/enum.properties b/sormas-api/src/main/resources/enum.properties
@@ -775,9 +775,9 @@ ExposureType.BURIAL=Burial
 ExposureType.ANIMAL_CONTACT=Animal Contact
 ExposureType.OTHER=Other
 ExposureType.UNKNOWN=Unknown
-ExposureType.RECREATIONAL_WATER=Exposure to recreational water
-ExposureType.FOOD=Exposure to food
-ExposureType.SEXUAL_CONTACT=Sexual exposure
+ExposureType.RECREATIONAL_WATER=Recreational water
+ExposureType.FOOD=Food
+ExposureType.SEXUAL_CONTACT=Sexual contact
 ExposureType.SYMPTOMATIC_CONTACT=Contact with symptomatic individuals
 ExposureType.FLOOD_EXPOSURE=Flooded area
 
diff --git a/sormas-backend/src/main/resources/sql/sormas_schema.sql b/sormas-backend/src/main/resources/sql/sormas_schema.sql
@@ -14820,4 +14820,11 @@ ALTER TABLE symptoms_history ALTER COLUMN timeoffworkdays TYPE float4 USING time
 ALTER TABLE healthconditions_history DROP COLUMN IF EXISTS immunodepression;
 
 INSERT INTO schema_version (version_number, comment) VALUES (595, 'RSV issue fixes and minor observations of Giardiasis and Cryptosporidiosis #13540 #13613');
+
+-- 2025-10-29 - Included new Disease variant/subtype for RSV #13543
+INSERT INTO customizableenumvalue(id, uuid, changedate, creationdate, datatype, value, caption, diseases)
+VALUES (nextval('entity_seq'), generate_base32_uuid(), now(), now(), 'DISEASE_VARIANT', 'INDETERMINATE', 'Indeterminate',
+        'RESPIRATORY_SYNCYTIAL_VIRUS');
+INSERT INTO schema_version (version_number, comment) VALUES (596, 'Included new Disease variant/subtype for RSV #13543');
+
 -- *** Insert new sql commands BEFORE this line. Remember to always consider _history tables. ***
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/caze/CaseDataForm.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/caze/CaseDataForm.java
@@ -476,6 +476,10 @@ protected void addFields() {
 		TextField diseaseVariantDetailsField = addField(CaseDataDto.DISEASE_VARIANT_DETAILS, TextField.class);
 		diseaseVariantDetailsField.setVisible(false);
 		diseaseVariantField.setNullSelectionAllowed(true);
+		if (disease == Disease.RESPIRATORY_SYNCYTIAL_VIRUS) {
+			diseaseVariantField.setCaption(I18nProperties.getCaption(Captions.PathogenTest_rsv_testedDiseaseVariant));
+			diseaseVariantDetailsField.setCaption(I18nProperties.getCaption(Captions.PathogenTest_rsv_testedDiseaseVariantDetails));
+		}
 		addField(CaseDataDto.DISEASE_DETAILS, TextField.class);
 		addField(CaseDataDto.PLAGUE_TYPE, NullableOptionGroup.class);
 		addField(CaseDataDto.DENGUE_FEVER_TYPE, NullableOptionGroup.class);
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/events/EventDataForm.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/events/EventDataForm.java
@@ -259,8 +259,8 @@ protected void addFields() {
 			EventDto.EVENT_INVESTIGATION_STATUS,
 			Arrays.asList(EventInvestigationStatus.ONGOING, EventInvestigationStatus.DONE, EventInvestigationStatus.DISCARDED),
 			true);
-		DateComparisonValidator.addStartEndValidators(investigationStartDate, investigationEndDate, false);
-		DateComparisonValidator.addStartEndValidators(startDate, investigationStartDate, false);
+		DateComparisonValidator.addStartEndValidators(investigationStartDate, investigationEndDate, true);
+		DateComparisonValidator.addStartEndValidators(startDate, investigationStartDate, true);
 		TextField title = addField(EventDto.EVENT_TITLE, TextField.class);
 		title.addStyleName(CssStyles.SOFT_REQUIRED);
 
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/hospitalization/HospitalizationForm.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/hospitalization/HospitalizationForm.java
@@ -247,8 +247,15 @@ protected void addFields() {
 		initializeAccessAndAllowedAccesses();
 
 		if (List.of(Disease.GIARDIASIS, Disease.CRYPTOSPORIDIOSIS).contains(caze.getDisease())) {
-			FieldHelper
-				.setRequiredWhenNotNull(getFieldGroup(), HospitalizationDto.ADMITTED_TO_HEALTH_FACILITY, HospitalizationDto.HOSPITALIZATION_REASON);
+			// Make hospitalization reason required when admitted to health facility or currently hospitalized
+			admittedToHealthFacilityField.addValueChangeListener(e -> {
+				YesNoUnknown value = (YesNoUnknown) admittedToHealthFacilityField.getNullableValue();
+				hospitalizationReason.setRequired(value == YesNoUnknown.YES);
+			});
+			currentlyHospitalizedField.addValueChangeListener(e -> {
+				YesNoUnknown value = (YesNoUnknown) currentlyHospitalizedField.getNullableValue();
+				hospitalizationReason.setRequired(value == YesNoUnknown.YES);
+			});
 			durationOfHospitalization.setVisible(true);
 		}
 
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/AbstractSampleForm.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/AbstractSampleForm.java
@@ -285,7 +285,7 @@ protected void addValidators() {
 			new DateComparisonValidator(
 				shipmentDate,
 				sampleDateField,
-				false,
+				true,
 				false,
 				I18nProperties.getValidationError(Validations.afterDate, shipmentDate.getCaption(), sampleDateField.getCaption())));
 		shipmentDate.addValidator(
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestForm.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestForm.java
@@ -23,6 +23,8 @@
 import static de.symeda.sormas.ui.utils.LayoutUtil.fluidRowLocs;
 import static de.symeda.sormas.ui.utils.LayoutUtil.loc;
 
+import java.time.LocalTime;
+import java.time.ZoneId;
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Date;
@@ -302,7 +304,7 @@ public void setValue(PathogenTestDto newFieldValue) throws ReadOnlyException, Co
 		testTypeField.setValue(newFieldValue.getTestType());
 		pcrTestSpecification.setValue(newFieldValue.getPcrTestSpecification());
 		testTypeTextField.setValue(newFieldValue.getTestTypeText());
-		if(!testResultField.isReadOnly()) {
+		if (!testResultField.isReadOnly()) {
 			testResultField.setValue(newFieldValue.getTestResult());
 		}
 		typingIdField.setValue(newFieldValue.getTypingId());
@@ -331,17 +333,37 @@ protected void addFields() {
 		testTypeTextField = addField(PathogenTestDto.TEST_TYPE_TEXT, TextField.class);
 		FieldHelper.addSoftRequiredStyle(testTypeTextField);
 		DateTimeField testDateField = addField(PathogenTestDto.TEST_DATE_TIME, DateTimeField.class);
+		testDateField.removeAllValidators();
 		testDateField.addValidator(
 			new DateComparisonValidator(
 				testDateField,
 				this::getSampleDate,
 				false,
 				false,
+				true,
 				I18nProperties.getValidationError(
 					Validations.afterDateWithDate,
 					testDateField.getCaption(),
 					I18nProperties.getPrefixCaption(SampleDto.I18N_PREFIX, SampleDto.SAMPLE_DATE_TIME),
 					DateFormatHelper.formatDate(getSampleDate()))));
+		testDateField.addValueChangeListener(e -> {
+			boolean hasTime = !getSampleDate().toInstant().atZone(ZoneId.systemDefault()).toLocalDate().equals(LocalTime.MIDNIGHT);
+			if (hasTime) {
+				testDateField.removeAllValidators();
+				testDateField.addValidator(
+					new DateComparisonValidator(
+						testDateField,
+						this::getSampleDate,
+						false,
+						false,
+						false,
+						I18nProperties.getValidationError(
+							Validations.afterDateWithDate,
+							testDateField.getCaption(),
+							I18nProperties.getPrefixCaption(SampleDto.I18N_PREFIX, SampleDto.SAMPLE_DATE_TIME),
+							DateFormatHelper.formatLocalDateTime(getSampleDate()))));
+			}
+		});
 		ComboBox lab = addInfrastructureField(PathogenTestDto.LAB);
 		lab.addItems(FacadeProvider.getFacilityFacade().getAllActiveLaboratories(true));
 		TextField labDetails = addField(PathogenTestDto.LAB_DETAILS, TextField.class);
@@ -354,9 +376,13 @@ protected void addFields() {
 		addField(PathogenTestDto.TESTED_DISEASE_DETAILS, TextField.class);
 		ComboBox diseaseVariantField = addCustomizableEnumField(PathogenTestDto.TESTED_DISEASE_VARIANT);
 		diseaseVariantField.setNullSelectionAllowed(true);
+		diseaseVariantField.setVisible(false);
 		TextField diseaseVariantDetailsField = addField(PathogenTestDto.TESTED_DISEASE_VARIANT_DETAILS, TextField.class);
 		diseaseVariantDetailsField.setVisible(false);
-
+		if (disease == Disease.RESPIRATORY_SYNCYTIAL_VIRUS) {
+			diseaseVariantField.setCaption(I18nProperties.getCaption(Captions.PathogenTest_rsv_testedDiseaseVariant));
+			diseaseVariantDetailsField.setCaption(I18nProperties.getCaption(Captions.PathogenTest_rsv_testedDiseaseVariantDetails));
+		}
 		ComboBox genoTypingCB = addField(PathogenTestDto.GENOTYPE_RESULT, ComboBox.class);
 		genoTypingCB.setVisible(true);
 		TextField genoTypingResultTextTF = addField(PathogenTestDto.GENOTYPE_RESULT_TEXT, TextField.class);
@@ -492,7 +518,11 @@ protected void addFields() {
 				{
 					put(
 						PathogenTestDto.TESTED_DISEASE,
-						Arrays.asList(Disease.TUBERCULOSIS, Disease.LATENT_TUBERCULOSIS, Disease.INVASIVE_MENINGOCOCCAL_INFECTION, Disease.INVASIVE_PNEUMOCOCCAL_INFECTION));
+						Arrays.asList(
+							Disease.TUBERCULOSIS,
+							Disease.LATENT_TUBERCULOSIS,
+							Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
+							Disease.INVASIVE_PNEUMOCOCCAL_INFECTION));
 					put(PathogenTestDto.TEST_TYPE, Arrays.asList(PathogenTestType.ANTIBIOTIC_SUSCEPTIBILITY));
 				}
 			};
@@ -503,7 +533,11 @@ protected void addFields() {
 				{
 					put(
 						PathogenTestDto.TESTED_DISEASE,
-						Arrays.asList(Disease.TUBERCULOSIS, Disease.LATENT_TUBERCULOSIS, Disease.INVASIVE_MENINGOCOCCAL_INFECTION, Disease.INVASIVE_PNEUMOCOCCAL_INFECTION));
+						Arrays.asList(
+							Disease.TUBERCULOSIS,
+							Disease.LATENT_TUBERCULOSIS,
+							Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
+							Disease.INVASIVE_PNEUMOCOCCAL_INFECTION));
 					put(
 						PathogenTestDto.TEST_TYPE,
 						Arrays.asList(
@@ -1037,6 +1071,17 @@ protected void addFields() {
 		FieldHelper
 			.setVisibleWhen(getFieldGroup(), PathogenTestDto.GENOTYPE_RESULT_TEXT, PathogenTestDto.GENOTYPE_RESULT, GenoTypeResult.OTHER, true);
 
+		//RSV subtype specification
+		Map<Object, List<Object>> rsvSubTypeDependencies = new HashMap<>() {
+
+			{
+				put(PathogenTestDto.TESTED_DISEASE, Arrays.asList(Disease.RESPIRATORY_SYNCYTIAL_VIRUS));
+				put(PathogenTestDto.TEST_TYPE, Arrays.asList(PathogenTestType.SEQUENCING, PathogenTestType.WHOLE_GENOME_SEQUENCING));
+				put(PathogenTestDto.TEST_RESULT, Arrays.asList(PathogenTestResultType.POSITIVE));
+			}
+		};
+		FieldHelper.setVisibleWhen(getFieldGroup(), PathogenTestDto.TESTED_DISEASE_VARIANT, rsvSubTypeDependencies, true);
+
 		Consumer<Disease> updateDiseaseVariantField = disease -> {
 			List<DiseaseVariant> diseaseVariants =
 				FacadeProvider.getCustomizableEnumFacade().getEnumValues(CustomizableEnumType.DISEASE_VARIANT, disease);
@@ -1103,7 +1148,7 @@ protected void addFields() {
 			ImmutableList.of(PathogenTestType.GENOTYPING));
 
 		BiConsumer<Disease, PathogenTestType> resultField = (disease, testType) -> {
-			if(testResultField.isReadOnly()) {
+			if (testResultField.isReadOnly()) {
 				return;
 			}
 			if (resultFieldDecisionMap.containsKey(disease) && resultFieldDecisionMap.get(disease).contains(testType)) {
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/pathogentestlink/PathogenTestListEntry.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/samples/pathogentestlink/PathogenTestListEntry.java
@@ -105,6 +105,7 @@ public PathogenTestListEntry(PathogenTestDto pathogenTest, boolean showTestResul
 
 			if (pathogenTest.getTestedDiseaseVariant() != null) {
 				Label labelBottomLeft = new Label(pathogenTest.getTestedDiseaseVariant().toString());
+				CssStyles.style(labelBottomLeft, CssStyles.LABEL_BOLD, CssStyles.LABEL_UPPERCASE, CssStyles.LABEL_CRITICAL);
 				bottomLabelLayout.addComponent(labelBottomLeft);
 			}
 
diff --git a/sormas-ui/src/main/java/de/symeda/sormas/ui/utils/DateComparisonValidator.java b/sormas-ui/src/main/java/de/symeda/sormas/ui/utils/DateComparisonValidator.java
@@ -59,6 +59,32 @@ public DateComparisonValidator(
 		this.changeInvalidCommitted = changeInvalidCommitted;
 	}
 
+	/**
+	 * To compare the time along with dates, set dateOnly to false.
+	 * 
+	 * @param dateField
+	 * @param referenceDateSupplier
+	 * @param earlierOrSame
+	 * @param changeInvalidCommitted
+	 * @param dateOnly
+	 * @param errorMessage
+	 */
+	public DateComparisonValidator(
+		Field<Date> dateField,
+		Supplier<Date> referenceDateSupplier,
+		boolean earlierOrSame,
+		boolean changeInvalidCommitted,
+		boolean dateOnly,
+		String errorMessage) {
+
+		super(errorMessage);
+		this.dateField = dateField;
+		this.referenceDateSupplier = referenceDateSupplier;
+		this.earlierOrSame = earlierOrSame;
+		this.dateOnly = dateOnly;
+		this.changeInvalidCommitted = changeInvalidCommitted;
+	}
+
 	public DateComparisonValidator(
 		Field<Date> dateField,
 		Supplier<Date> referenceDateSupplier,
@@ -94,7 +120,6 @@ public DateComparisonValidator(
 		this(dateField, () -> referenceDate, earlierOrSame, changeInvalidCommitted, errorMessage);
 	}
 
-
 	@Override
 	protected boolean isValidValue(Date date) {
 
