#13793 - Disabled classification popup for pathogen tests that are negative

The behaviour was introduced it seems by a requirement to display the
case classification popup for verified pathogen tests (positive and negative).

While the behaviour might have beed desired, the actual logic in the code and
popup text is not. The popup text and the logic in other blocks of the code lead
us to the conclusion that only positive results trigger the popup.

Author: raulbob

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

@@ -351,6 +351,33 @@ public void savePathogenTests(List<PathogenTestDto> pathogenTests, SampleReferen
 			TRAY_NOTIFICATION);
 	}
 
+	/**
+	 * Handles the association of a pathogen test with a case.
+	 * Based on pathogen test results the following logic is applied:
+	 * 
+	 * <p>Negative test result AND test result verified
+	 * <ol>
+	 * <li>Tested disease == case disease AND test result != sample pathogen test result: Ask user whether to update the sample pathogen test result</li>
+	 * <li>Tested disease != case disease: Do nothing</li>
+	 * </ol>
+	 * </p>
+	 * <p>Positive test result AND test result verified
+	 * <ol>
+	 * <li>Tested disease == case disease: Ask user whether to update the sample pathogen test result
+	 * <ol>
+	 * <li>Tested disease variant != case disease variant: Ask user to change the case disease variant</li>
+	 * <li>Case classification != confirmed: Ask user whether to confirm the case</li>
+	 * </ol>
+	 * </li>
+	 * <li>Tested disease != case disease: Ask user to create a new case for the tested disease</li>
+	 * </ol>
+	 * </p>
+	 * 
+	 * @param pathogenTests the pathogen tests
+	 * @param associatedCase the associated case
+	 * @param suppressNavigateToCase whether to suppress navigation to the case
+	 * 
+	*/
 	private void handleAssociatedCase(List<PathogenTestDto> pathogenTests, CaseReferenceDto associatedCase, boolean suppressNavigateToCase) {
 
 		if (!UiUtil.permitted(UserRight.CASE_EDIT)) {
@@ -367,46 +394,68 @@ private void handleAssociatedCase(List<PathogenTestDto> pathogenTests, CaseRefer
 		// a.2) Case classification != confirmed: Ask user whether to confirm the case
 		// b) Tested disease != case disease: Ask user to create a new case for the tested disease
 
-		CaseDataDto caze = FacadeProvider.getCaseFacade().getCaseDataByUuid(associatedCase.getUuid());
+		final CaseDataDto caze = FacadeProvider.getCaseFacade().getCaseDataByUuid(associatedCase.getUuid());
 
-		Map<Disease, List<PathogenTestDto>> testsByDisease = pathogenTests.stream().collect(Collectors.groupingBy(PathogenTestDto::getTestedDisease));
-		Optional<PathogenTestDto> positiveWithSameDisease = testsByDisease.getOrDefault(caze.getDisease(), Collections.emptyList())
+		final Map<Disease, List<PathogenTestDto>> testsByDisease =
+			pathogenTests.stream().collect(Collectors.groupingBy(PathogenTestDto::getTestedDisease));
+		final Optional<PathogenTestDto> positiveWithSameDisease = testsByDisease.getOrDefault(caze.getDisease(), Collections.emptyList())
 			.stream()
 			.filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified()))
 			.findFirst();
 
-		Optional<PathogenTestDto> negativeWithSameDisease = testsByDisease.getOrDefault(caze.getDisease(), Collections.emptyList())
+		final Optional<PathogenTestDto> negativeWithSameDisease = testsByDisease.getOrDefault(caze.getDisease(), Collections.emptyList())
 			.stream()
 			.filter(t -> t.getTestResult() == PathogenTestResultType.NEGATIVE && Boolean.TRUE.equals(t.getTestResultVerified()))
 			.findFirst();
 
-		PathogenTestDto resultedPathogenTest;
-		if (positiveWithSameDisease.isPresent()) {
-			resultedPathogenTest = positiveWithSameDisease.get();
-		} else if (negativeWithSameDisease.isPresent()) {
-			resultedPathogenTest = negativeWithSameDisease.get();
-		} else {
-			resultedPathogenTest = null;
-		}
+		final boolean hasVerifiedPositiveTest = positiveWithSameDisease.isPresent();
+		final boolean hasVerifiedNegativeTest = negativeWithSameDisease.isPresent();
+
+		final boolean hasVerifiedTests = hasVerifiedPositiveTest || hasVerifiedNegativeTest;
+
+
+		// 1. Ask user to update sample overall result if latest test result is different
+		// 2. Ask user to update disease variant if case variant is different
+		// 3. Ask user if they want to confirm the case only if any of the tests are verified either positive or negative (not pending or other)
+
+		// We need to display popups if any of the tests are verified either positive or negative
+		if (hasVerifiedTests) {
+			// get either the positive or negative test
+			final PathogenTestDto resultedPathogenTest = hasVerifiedPositiveTest ? positiveWithSameDisease.get() : negativeWithSameDisease.get();
+
+			// just a sanity check
+			if (resultedPathogenTest == null) {
+				throw new IllegalStateException("No verified test found for disease " + caze.getDisease());
+			}
 
-		if (resultedPathogenTest != null) {
-			showChangeAssociatedSampleResultDialog(resultedPathogenTest, (accepted) -> {
-				if (accepted) {
-					checkForDiseaseVariantUpdate(resultedPathogenTest, caze, suppressNavigateToCase, this::showConfirmCaseDialog);
+			showChangeAssociatedSampleResultDialog(resultedPathogenTest, accepted -> { // Change sample result
+				// Accepted SR may have changed
+				if (Boolean.TRUE.equals(accepted)) {
+					checkForDiseaseVariantUpdate(resultedPathogenTest, caze, suppressNavigateToCase, c -> { // Update disease variant
+						// Only show the confirmation dialog if there are verified positive tests
+						// We decided this based on the intented text in the dialog but based on the test results instead of the sample overall result
+						if (hasVerifiedPositiveTest) {
+							// The final laboratory result of the sample the saved pathogen test belongs to is positive. <-- sample overall result
+							// 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
+						}
+					});
 				}
 			});
 		}
 
 		testsByDisease.keySet().stream().filter(disease -> disease != caze.getDisease()).forEach((disease) -> {
 			List<PathogenTestDto> tests = testsByDisease.get(disease);
 
-			Optional<PathogenTestDto> positiveWithOtherDisease =
-				tests.stream().filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified())).findFirst();
+			Optional<PathogenTestDto> positiveWithOtherDisease = tests.stream()
+				.filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified()))
+				.findFirst();
 
 			if (positiveWithOtherDisease.isPresent()) {
 				List<CaseDataDto> duplicatedCases =
 					FacadeProvider.getCaseFacade().getDuplicatesWithPathogenTest(caze.getPerson(), positiveWithOtherDisease.get());
-				if (duplicatedCases == null || duplicatedCases.size() == 0) {
+				if (duplicatedCases == null || duplicatedCases.isEmpty()) {
 					PathogenTestDto positiveTestWithOtherDisease = positiveWithOtherDisease.get();
 
 					showCaseCloningWithNewDiseaseDialog(
@@ -466,8 +515,9 @@ private void handleAssociatedContact(List<PathogenTestDto> pathogenTests, Contac
 			testsByDisease.keySet().stream().filter(disease -> disease != contact.getDisease()).forEach((disease) -> {
 				List<PathogenTestDto> tests = testsByDisease.get(disease);
 
-				Optional<PathogenTestDto> positiveWithOtherDisease =
-					tests.stream().filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified())).findFirst();
+				Optional<PathogenTestDto> positiveWithOtherDisease = tests.stream()
+					.filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified()))
+					.findFirst();
 				if (positiveWithOtherDisease.isPresent()) {
 					List<CaseDataDto> duplicatedCases =
 						FacadeProvider.getCaseFacade().getDuplicatesWithPathogenTest(contact.getPerson(), positiveWithOtherDisease.get());
@@ -530,8 +580,9 @@ private void handleAssociatedEventParticipant(List<PathogenTestDto> pathogenTest
 			testsByDisease.keySet().stream().filter(disease -> disease != eventDisease).forEach((disease) -> {
 				List<PathogenTestDto> tests = testsByDisease.get(disease);
 
-				Optional<PathogenTestDto> positiveWithOtherDisease =
-					tests.stream().filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified())).findFirst();
+				Optional<PathogenTestDto> positiveWithOtherDisease = tests.stream()
+					.filter(t -> t.getTestResult() == PathogenTestResultType.POSITIVE && Boolean.TRUE.equals(t.getTestResultVerified()))
+					.findFirst();
 				if (positiveWithOtherDisease.isPresent() && UiUtil.enabled(FeatureType.CASE_SURVEILANCE)) {
 					List<CaseDataDto> duplicatedCases = FacadeProvider.getCaseFacade()
 						.getDuplicatesWithPathogenTest(eventParticipant.getPerson().toReference(), positiveWithOtherDisease.get());
@@ -616,7 +667,7 @@ public void showConvertEventParticipantToCaseDialog(EventParticipantDto eventPar
 			I18nProperties.getString(Strings.no),
 			800,
 			confirmed -> {
-				if (confirmed) {
+				if (Boolean.TRUE.equals(confirmed)) {
 					if (differentDiseases) {
 						ControllerProvider.getCaseController().createFromEventParticipantDifferentDisease(eventParticipant, testedDisease);
 					} else {
@@ -635,7 +686,7 @@ public void showConvertContactToCaseDialog(ContactDto contact, Consumer<Boolean>
 			I18nProperties.getString(Strings.no),
 			800,
 			confirmed -> {
-				if (confirmed) {
+				if (Boolean.TRUE.equals(confirmed)) {
 					ControllerProvider.getCaseController().createFromContact(contact);
 				}
 				callback.accept(confirmed);
@@ -650,7 +701,7 @@ public void showCreateContactCaseDialog(ContactDto contact, Disease disease) {
 			I18nProperties.getString(Strings.no),
 			800,
 			confirmed -> {
-				if (confirmed) {
+				if (Boolean.TRUE.equals(confirmed)) {
 					ControllerProvider.getCaseController().createFromUnrelatedContact(contact, disease);
 				}
 			});
@@ -670,7 +721,7 @@ public static void showCaseCloningWithNewDiseaseDialog(
 			I18nProperties.getString(Strings.no),
 			800,
 			confirmed -> {
-				if (confirmed) {
+				if (Boolean.TRUE.equals(confirmed)) {
 					existingCaseDto.setCaseClassification(CaseClassification.NOT_CLASSIFIED);
 					existingCaseDto.setClassificationUser(null);
 					existingCaseDto.setDisease(disease);
@@ -702,7 +753,7 @@ public void showConfirmCaseDialog(CaseDataDto caze) {
 			I18nProperties.getString(Strings.no),
 			800,
 			confirmed -> {
-				if (confirmed) {
+				if (Boolean.TRUE.equals(confirmed)) {
 					CaseDataDto caseDataByUuid = FacadeProvider.getCaseFacade().getCaseDataByUuid(caze.getUuid());
 					caseDataByUuid.setCaseClassification(CaseClassification.CONFIRMED);
 					FacadeProvider.getCaseFacade().save(caseDataByUuid);