Merge pull request #13985 from SORMAS-Foundation/bugfix-negative-test-results-updates-caseclassification

Fixed the case classification when a negative test result is detected.

Author: KarnaiahPesula

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Captions.java

@@ -921,6 +921,7 @@ public interface Captions {
 	String caseLinkToSamples = "caseLinkToSamples";
 	String caseMergeDuplicates = "caseMergeDuplicates";
 	String caseMinusDays = "caseMinusDays";
+	String caseNegativeCase = "caseNegativeCase";
 	String caseNewCase = "caseNewCase";
 	String caseNewCaseDate = "caseNewCaseDate";
 	String caseNoDiseaseVariant = "caseNoDiseaseVariant";

sormas-api/src/main/java/de/symeda/sormas/api/i18n/Strings.java

@@ -1554,6 +1554,7 @@ public interface Strings {
 	String messageMissingDateFilter = "messageMissingDateFilter";
 	String messageMissingEpiWeekFilter = "messageMissingEpiWeekFilter";
 	String messageMultipleSampleReports = "messageMultipleSampleReports";
+	String messageNegativeCaseAfterPathogenTest = "messageNegativeCaseAfterPathogenTest";
 	String messageNoCaseFound = "messageNoCaseFound";
 	String messageNoCaseFoundToLinkImmunization = "messageNoCaseFoundToLinkImmunization";
 	String messageNoCasesSelected = "messageNoCasesSelected";

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

@@ -409,6 +409,7 @@ caseCalculateCompleteness=Calculate completeness
 caseClassificationCalculationButton=Calculate case classification
 caseNumberOfDuplicatesDetected=%d potential duplicates detected
 caseConfirmCase=Confirm case
+caseNegativeCase=Negative case
 convertEventParticipantToCase=Create case from event participant with positive test result?
 convertContactToCase=Create case from contact with positive test result?
 caseSearchSpecificCase=Search specific case

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

@@ -1243,6 +1243,7 @@ messageCloneCaseWithNewDisease = You have just created a positive pathogen test
 messageUpdateCaseWithNewDiseaseVariant = You have saved a positive pathogen test of a different disease variant than the variant specified in the case. Do you want to update the disease variant of the case? The case's current disease variant is %s, the pathogen test's disease variant is %s.
 messageCompletenessValuesUpdated = Completeness values have been updated.
 messageConfirmCaseAfterPathogenTest=The final laboratory result of the sample the saved pathogen test belongs to is positive. However, the case cannot be automatically classified as a confirmed case because it is missing some information. Do you want to set the case classification to confirmed anyway?
+messageNegativeCaseAfterPathogenTest=The final laboratory result of the sample the saved pathogen test belongs to is negative. However, the case cannot be automatically classified as not a case because it is missing some information. Do you want to set the case classification to not a case anyway?
 messageConvertContactToCase=You have just saved a positive laboratory result for the contact disease. Do you want to create a case for the contact person? The case will be set as the resulting case of this contact, and the final laboratory result of the sample will automatically be set to positive.
 messageConvertContactToCaseDifferentDiseases=You have just saved a positive laboratory result for a different disease than the contact disease. Do you want to create a case with this disease for the contact person? The case will not be set as the resulting case of this contact.
 messageConvertEventParticipantToCase=You have just saved a positive laboratory result for the event disease. Do you want to create a case for the event participant person? The case will automatically be linked to the event participant, and the final laboratory result of the sample will be set to positive.

sormas-backend/src/main/java/de/symeda/sormas/backend/caze/classification/CaseClassificationFacadeEjb.java

@@ -554,7 +554,7 @@ private void buildCriteria() {
 				symptom(SymptomsDto.ABDOMINAL_PAIN),
 				symptom(SymptomsDto.WEIGHT_LOSS)),
 			xOf(1, (positiveTestResult(Disease.GIARDIASIS, PathogenTestType.MICROSCOPY, PathogenTestType.PCR_RT_PCR, PathogenTestType.CULTURE))));
-		addCriteria(Disease.GIARDIASIS, DateHelper.getDateZero(2020, 11, 6), null, probable, confirmed, null);
+		addCriteria(Disease.GIARDIASIS, DateHelper.getDateZero(2020, 11, 6), null, probable, confirmed, notACase(Disease.GIARDIASIS));
 
 		// Cryptosporidiosis
 		probable = allOf(
@@ -572,7 +572,7 @@ private void buildCriteria() {
 			xOf(
 				1,
 				(positiveTestResult(Disease.CRYPTOSPORIDIOSIS, PathogenTestType.MICROSCOPY, PathogenTestType.PCR_RT_PCR, PathogenTestType.CULTURE))));
-		addCriteria(Disease.CRYPTOSPORIDIOSIS, DateHelper.getDateZero(2020, 11, 6), null, probable, confirmed, null);
+		addCriteria(Disease.CRYPTOSPORIDIOSIS, DateHelper.getDateZero(2020, 11, 6), null, probable, confirmed, notACase(Disease.CRYPTOSPORIDIOSIS));
 
 		// CORONAVIRUS
 		suspect = xOf(

sormas-ui/src/main/java/de/symeda/sormas/ui/contact/ContactDataView.java

@@ -228,9 +228,9 @@ protected void initView(String params) {
 			taskList.addStyleName(CssStyles.SIDE_COMPONENT);
 			layout.addSidePanelComponent(taskList, TASKS_LOC);
 		}
-
+		// Allowing the samples component for LUX Measles.
 		if (!(FacadeProvider.getConfigFacade().isConfiguredCountry(CountryHelper.COUNTRY_CODE_LUXEMBOURG)
-			&& List.of(Disease.INVASIVE_MENINGOCOCCAL_INFECTION, Disease.MEASLES).contains(contactDto.getDisease()))) {
+			&& List.of(Disease.INVASIVE_MENINGOCOCCAL_INFECTION).contains(contactDto.getDisease()))) {
 			if (UiUtil.permitted(UserRight.SAMPLE_VIEW)) {
 				SampleListComponent sampleList = new SampleListComponent(
 					new SampleCriteria().contact(getContactRef())
@@ -257,7 +257,8 @@ protected void initView(String params) {
 		}
 
 		// Immunizations are not shown for Salmonellosis contacts
-		if (UiUtil.permitted(FeatureType.IMMUNIZATION_MANAGEMENT, UserRight.IMMUNIZATION_VIEW) && !IMMUNIZATION_EXCLUDED_DISEASES.contains(resolvedDisease)) {
+		if (UiUtil.permitted(FeatureType.IMMUNIZATION_MANAGEMENT, UserRight.IMMUNIZATION_VIEW)
+			&& !IMMUNIZATION_EXCLUDED_DISEASES.contains(resolvedDisease)) {
 			final VaccinationStatusPanel vaccinationStatusPanel = VaccinationStatusPanel.forContact(contactDto);
 			if (contactDto.getVaccinationStatusLastUpdated() == null && UiUtil.permitted(UserRight.IMMUNIZATION_EDIT)) {
 				showVaccinationStatusUpdateDialog(contactDto);

sormas-ui/src/main/java/de/symeda/sormas/ui/samples/PathogenTestController.java

@@ -458,6 +458,14 @@ private void handleAssociatedCase(List<PathogenTestDto> pathogenTests, CaseRefer
 							// However, the case cannot be automatically classified as a confirmed case because it is missing some information.
 							// Do you want to set the case classification to confirmed anyway?
 							this.showConfirmCaseDialog(c); // Case classification
+						} else if (hasVerifiedNegativeTest) {
+							// Show the confirmation dialog if there are verified negative tests.
+							// The final laboratory result of the sample the saved pathogen test belongs to is negative. <-- sample overall result
+							// However, the case cannot be automatically classified as not a case because it is missing some information.
+							// Do you want to set the case classification to not a case anyway?
+							this.showNegativeCaseDialog(caze);
+						} else {
+							// for other cases, no information is required.
 						}
 					});
 				}
@@ -780,4 +788,35 @@ public void showConfirmCaseDialog(CaseDataDto caze) {
 				}
 			});
 	}
+
+	/**
+	 * When the test result is negative, the case is not "confirmed" anymore, but the user might want to update the case classification to
+	 * confirmed or not a case for the negative test result. This dialog offers this option to the user.
+	 * If the user accepts the case classification change, then it'll be updated with not a case, otherwise
+	 * no change to the existing classification.
+	 * 
+	 * @param caze
+	 */
+	public void showNegativeCaseDialog(CaseDataDto caze) {
+		//  This is applicable for all countries.
+		// if the case is already not a case, then no need to show the dialog
+		if (caze.getCaseClassification() == CaseClassification.NO_CASE) {
+			return;
+		}
+
+		VaadinUiUtil.showConfirmationPopup(
+			I18nProperties.getCaption(Captions.caseNegativeCase),
+			new Label(I18nProperties.getString(Strings.messageNegativeCaseAfterPathogenTest)),
+			I18nProperties.getString(Strings.yes),
+			I18nProperties.getString(Strings.no),
+			800,
+			confirmed -> {
+				if (Boolean.TRUE.equals(confirmed)) {
+					CaseDataDto caseDataByUuid = FacadeProvider.getCaseFacade().getCaseDataByUuid(caze.getUuid());
+					caseDataByUuid.setCaseClassification(CaseClassification.NO_CASE);
+					FacadeProvider.getCaseFacade().save(caseDataByUuid);
+					ControllerProvider.getCaseController().navigateToCase(caseDataByUuid.getUuid());
+				}
+			});
+	}
 }