Merge pull request #13878 from SORMAS-Foundation/feature/13858-tube-field-handler

Pathogen Test Form Refactor (Part 1)

Author: roldy

sormas-api/src/main/java/de/symeda/sormas/api/utils/Diseases.java

@@ -90,6 +90,12 @@ public static boolean isDefined(Class<?> clazz, String propertyName, Disease dis
 			return diseaseConfig.get(propertyName).contains(disease);
 		}
 
+		public static <E extends Enum<E>> List<E> getVisibleValues(Class<E> enumClass, Disease disease) {
+			return Arrays.stream(enumClass.getEnumConstants())
+				.filter(e -> isDefinedOrMissing(enumClass, e.name(), disease))
+				.collect(Collectors.toList());
+		}
+
 		private static synchronized void readDiseaseConfig(Class<?> clazz) {
 
 			HashMap<String, List<Disease>> diseaseConfig = new HashMap<>();

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

@@ -15770,4 +15770,4 @@ UPDATE diseaseconfiguration SET exposurecategories = 'VECTOR_BORNE' WHERE diseas
 
 INSERT INTO schema_version (version_number, comment) VALUES (622, '#13887 default disease exposure category configuration');
 
--- *** Insert new sql commands BEFORE this line. Remember to always consider _history tables. ***
+-- *** Insert new sql commands BEFORE this line. Remember to always consider _history tables. ***

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

@@ -42,7 +42,6 @@
 import de.symeda.sormas.api.caze.CaseClassification;
 import de.symeda.sormas.api.caze.CaseDataDto;
 import de.symeda.sormas.api.caze.CaseReferenceDto;
-import de.symeda.sormas.api.common.DeletionReason;
 import de.symeda.sormas.api.contact.ContactDto;
 import de.symeda.sormas.api.contact.ContactReferenceDto;
 import de.symeda.sormas.api.contact.ContactStatus;
@@ -137,10 +136,10 @@ public CommitDiscardWrapperComponent<PathogenTestForm> getPathogenTestCreateComp
 			ContactDto contact = FacadeProvider.getContactFacade().getByUuid(sampleDto.getAssociatedContact().getUuid());
 			associatedEventOrCaseOrContactDisease = contact.getDisease();
 		}
-		PathogenTestForm createForm = new PathogenTestForm(sampleDto, true, caseSampleCount, false, true, associatedEventOrCaseOrContactDisease); // Valid because jurisdiction doesn't matter for entities that are about to be created
-		// Defaulting the case disease as tested disease
+		PathogenTestForm createForm = new PathogenTestForm(sampleDto, true, caseSampleCount, false, true, associatedEventOrCaseOrContactDisease);
 		pathogenTest.setTestedDisease(associatedEventOrCaseOrContactDisease);
 		createForm.setValue(pathogenTest);
+
 		final CommitDiscardWrapperComponent<PathogenTestForm> editView =
 			new CommitDiscardWrapperComponent<>(createForm, UiUtil.permitted(UserRight.PATHOGEN_TEST_CREATE), createForm.getFieldGroup());
 
@@ -254,10 +253,7 @@ public CommitDiscardWrapperComponent<PathogenTestForm> getPathogenTestEditCompon
 			});
 
 			if (pathogenTest.isDeleted()) {
-				editView.getWrappedComponent().getField(PathogenTestDto.DELETION_REASON).setVisible(true);
-				if (editView.getWrappedComponent().getField(PathogenTestDto.DELETION_REASON).getValue() == DeletionReason.OTHER_REASON) {
-					editView.getWrappedComponent().getField(PathogenTestDto.OTHER_DELETION_REASON).setVisible(true);
-				}
+				editView.getWrappedComponent().showDeletionInfo(pathogenTest.getDeletionReason());
 			}
 			editView.restrictEditableComponentsOnEditView(
 				forHumanSample ? UserRight.SAMPLE_EDIT : UserRight.ENVIRONMENT_SAMPLE_EDIT,
@@ -354,14 +350,17 @@ public void savePathogenTests(List<PathogenTestDto> pathogenTests, SampleReferen
 	/**
 	 * 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
+	 *
+	 * <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 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
+	 * <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>
@@ -372,12 +371,15 @@ public void savePathogenTests(List<PathogenTestDto> pathogenTests, SampleReferen
 	 * <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
-	 * 
-	*/
+	 *
+	 * @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)) {
@@ -413,7 +415,6 @@ private void handleAssociatedCase(List<PathogenTestDto> pathogenTests, CaseRefer
 
 		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)
@@ -436,7 +437,7 @@ private void handleAssociatedCase(List<PathogenTestDto> pathogenTests, CaseRefer
 						// 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. 
+							// 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
 						}