Fixes related tests & sample testing issues

 - #14025
 - #14023
 - #14034
 - #14026
 - #14031
 - #14024

Author: roldy

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

@@ -2431,6 +2431,7 @@ public interface Captions {
 	String PathogenTest_rifampicinResistant = "PathogenTest.rifampicinResistant";
 	String PathogenTest_rsv_testedDiseaseVariant = "PathogenTest.rsv.testedDiseaseVariant";
 	String PathogenTest_rsv_testedDiseaseVariantDetails = "PathogenTest.rsv.testedDiseaseVariantDetails";
+	String PathogenTest_rsvSubtype = "PathogenTest.rsvSubtype";
 	String PathogenTest_seroGrouping_INVASIVE_PNEUMOCOCCAL_INFECTION = "PathogenTest.seroGrouping.INVASIVE_PNEUMOCOCCAL_INFECTION";
 	String PathogenTest_seroGroupSpecification = "PathogenTest.seroGroupSpecification";
 	String PathogenTest_seroGroupSpecificationText = "PathogenTest.seroGroupSpecificationText";

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

@@ -43,8 +43,12 @@ public enum PathogenTestType {
 	@NotSelectableForNewTests
 	ANTIBODY_DETECTION,
 
+	// Resurrected for new-test selection (#14026 Measles, #14031 Giardia): scoped to the requesting diseases.
+	@Diseases(value = {
+		Disease.MEASLES,
+		Disease.GIARDIASIS })
 	@PathogenTestCategoryRel(PathogenTestCategory.ANTIGEN_DETECTION)
-	@NotSelectableForNewTests
+	@ResultValueTypeRel(ResultValueType.QUALITATIVE)
 	ANTIGEN_DETECTION,
 
 	// Merged Culture entry (bacterial + fungal) — supersedes BACTERIAL_CULTURE / FUNGAL_CULTURE for new
@@ -118,19 +122,11 @@ public enum PathogenTestType {
 	@NotSelectableForNewTests
 	MICROSCOPY,
 
+	// Resurrected for IMI new-test selection (#14034): scoped to Invasive Meningococcal Infection only.
 	@Diseases(value = {
-		Disease.RESPIRATORY_SYNCYTIAL_VIRUS,
-		Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
-		Disease.INVASIVE_PNEUMOCOCCAL_INFECTION,
-		Disease.MEASLES,
-		Disease.GIARDIASIS,
-		Disease.CRYPTOSPORIDIOSIS,
-		Disease.DENGUE,
-		Disease.MALARIA,
-		Disease.SALMONELLOSIS,
-		Disease.SHIGELLOSIS }, hide = true)
+		Disease.INVASIVE_MENINGOCOCCAL_INFECTION })
 	@PathogenTestCategoryRel(PathogenTestCategory.ANTIGEN_DETECTION)
-	@NotSelectableForNewTests
+	@ResultValueTypeRel(ResultValueType.QUALITATIVE)
 	LATEX_AGGLUTINATION,
 
 	@Diseases(value = {
@@ -347,6 +343,12 @@ public enum PathogenTestType {
 	@ResultValueTypeRel(ResultValueType.TEXT)
 	GENOTYPING,
 
+	@Diseases(value = {
+		Disease.RESPIRATORY_SYNCYTIAL_VIRUS })
+	@PathogenTestCategoryRel(PathogenTestCategory.MOLECULAR_ASSAYS)
+	@ResultValueTypeRel(ResultValueType.QUALITATIVE)
+	RSV_SUBTYPING,
+
 	@Diseases(value = {
 		Disease.TUBERCULOSIS,
 		Disease.LATENT_TUBERCULOSIS })
@@ -440,7 +442,8 @@ public enum PathogenTestType {
 
 	@Diseases(value = {
 		Disease.RESPIRATORY_SYNCYTIAL_VIRUS,
-		Disease.DENGUE })
+		Disease.DENGUE,
+		Disease.GIARDIASIS })
 	@PathogenTestCategoryRel(PathogenTestCategory.ANTIGEN_DETECTION)
 	@ResultValueTypeRel(ResultValueType.QUALITATIVE)
 	RAPID_ANTIGEN_DETECTION,

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

@@ -310,15 +310,12 @@ public enum SampleMaterial {
 		Disease.RESPIRATORY_SYNCYTIAL_VIRUS,
 		Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
 		Disease.INVASIVE_PNEUMOCOCCAL_INFECTION,
-		Disease.MEASLES,
 		Disease.GIARDIASIS,
 		Disease.CRYPTOSPORIDIOSIS,
 		Disease.MALARIA,
 		Disease.DENGUE,
 		Disease.SALMONELLOSIS,
 		Disease.SHIGELLOSIS }, hide = true)
-	@HideForCountries(countries = {
-		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	OP_ASPIRATE,
 
 	@Diseases(value = {
@@ -330,8 +327,6 @@ public enum SampleMaterial {
 		Disease.DENGUE,
 		Disease.SALMONELLOSIS,
 		Disease.SHIGELLOSIS }, hide = true)
-	@HideForCountries(countries = {
-		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	NP_ASPIRATE,
 
 	@Diseases(value = {
@@ -346,13 +341,13 @@ public enum SampleMaterial {
 		Disease.SHIGELLOSIS }, hide = true)
 	PLEURAL_FLUID,
 
+	// Re-activated for RSV new samples (#14023): the RSV specimen requirements list Nasopharyngeal lavage.
+	// No canonical SNOMED-CT code on the specimen sheet, so its SNOMED export stays null. 
 	@Diseases(value = {
 		Disease.RESPIRATORY_SYNCYTIAL_VIRUS })
-	@Deprecated
 	NASOPHARYNGEAL_LAVAGE,
 
 	@Diseases(value = {
-		Disease.RESPIRATORY_SYNCYTIAL_VIRUS,
 		Disease.INVASIVE_MENINGOCOCCAL_INFECTION,
 		Disease.INVASIVE_PNEUMOCOCCAL_INFECTION,
 		Disease.GIARDIASIS,
@@ -372,8 +367,6 @@ public enum SampleMaterial {
 		Disease.DENGUE,
 		Disease.SALMONELLOSIS,
 		Disease.SHIGELLOSIS }, hide = true)
-	@HideForCountries(countries = {
-		CountryHelper.COUNTRY_CODE_LUXEMBOURG })
 	AMNIOTIC_FLUID,
 
 	@Diseases(value = {
@@ -499,12 +492,12 @@ public enum SampleMaterial {
 	@Diseases(value = {
 		Disease.SALMONELLOSIS,
 		Disease.SHIGELLOSIS,
-			Disease.DENGUE}, hide = true)
+		Disease.DENGUE }, hide = true)
 	BONE,
 
 	@Diseases(value = {
 		Disease.SHIGELLOSIS,
-			Disease.DENGUE}, hide = true)
+		Disease.DENGUE }, hide = true)
 	BONE_MARROW,
 
 	@Diseases(value = {
@@ -546,7 +539,7 @@ public enum SampleMaterial {
 	@Diseases(value = {
 		Disease.SALMONELLOSIS,
 		Disease.SHIGELLOSIS,
-			Disease.DENGUE}, hide = true)
+		Disease.DENGUE }, hide = true)
 	LUNG_TISSUE,
 
 	@Diseases(value = {
@@ -639,8 +632,8 @@ public enum SampleMaterial {
 	 * new samples. This set is the runtime index used by {@link #isDeprecated()}; it must stay in sync
 	 * with the {@code @Deprecated} constants above.
 	 */
-	private static final Set<SampleMaterial> DEPRECATED_MATERIALS = Collections.unmodifiableSet(
-		EnumSet.of(URINE_PM, CORNEA_PM, NASAL_SWAB, NASOPHARYNGEAL_LAVAGE, THROAT_SWAB, THROAT_ASPIRATE, SOFT_TISSUE, BONE_AND_JOINT, OTHER));
+	private static final Set<SampleMaterial> DEPRECATED_MATERIALS =
+		Collections.unmodifiableSet(EnumSet.of(URINE_PM, CORNEA_PM, NASAL_SWAB, THROAT_SWAB, THROAT_ASPIRATE, SOFT_TISSUE, BONE_AND_JOINT, OTHER));
 
 	/**
 	 * @return SNOMED-CT code for this sample material, or {@code null} if no canonical code is mapped.

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

@@ -1998,6 +1998,7 @@ PathogenTest.seroGroupSpecification=Serogroup Specification
 PathogenTest.seroGroupSpecificationText=Specify Serogroup Specification Method
 PathogenTest.genoType=Genotype result
 PathogenTest.genoTypeText=Specify genotype text
+PathogenTest.rsvSubtype=RSV subtype
 PathogenTest.tubeNil=Tube Nil
 PathogenTest.tubeNilGT10=Tube Nil >10
 PathogenTest.tubeAgTb1=Tube Ag TB1

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

@@ -1275,6 +1275,7 @@ PathogenTestType.SLIDE_AGGLUTINATION = Slide Agglutination
 PathogenTestType.WHOLE_GENOME_SEQUENCING = Whole-Genome Sequencing (WGS)
 PathogenTestType.SEROGROUPING = Serogrouping
 PathogenTestType.GENOTYPING = Genotyping
+PathogenTestType.RSV_SUBTYPING = RSV subtyping
 PathogenTestType.RAPID_ANTIGEN_DETECTION = Rapid antigen detection test
 PathogenTestType.ENZYME_LINKED_IMMUNOSORBENT_ASSAY = Enzyme-linked immunosorbent assay (ELISA)
 PathogenTestType.NAAT = Nucleic acid amplification test (NAAT)
@@ -1470,7 +1471,7 @@ SampleMaterial.NP_ASPIRATE = Nasopharyngeal aspirate
 SampleMaterial.NP_SWAB = Nasopharyngeal swab
 SampleMaterial.NUCHAL_SKIN_BIOPSY = Nuchal skin biopsy
 SampleMaterial.OP_ASPIRATE = Oropharyngeal (throat) aspirate
-SampleMaterial.THROAT_SWAB = Oropharyngeal (throat) swab
+SampleMaterial.THROAT_SWAB = Oropharyngeal (throat) swab (old)
 SampleMaterial.PERITONEAL_FLUID = Peritoneal fluid
 SampleMaterial.PLASMA = Plasma
 SampleMaterial.PLEURAL_FLUID = Pleural fluid
@@ -1498,7 +1499,7 @@ SampleMaterial.NASAL_SWAB = Nasal swab
 SampleMaterial.OTHER = Other
 SampleMaterial.CORNEA_PM = Cornea p.m
 SampleMaterial.URINE_PM = Urine p.m
-SampleMaterial.OROPHARYNGEAL_SWAB = Oropharyngeal swab
+SampleMaterial.OROPHARYNGEAL_SWAB = Oropharyngeal (throat) swab
 SampleMaterial.THROAT_ASPIRATE = Throat aspirate
 SampleMaterial.NASOPHARYNGEAL_LAVAGE = Nasopharyngeal lavage
 SampleMaterial.INTESTINAL_FLUID = Intestinal fluid

sormas-api/src/test/java/de/symeda/sormas/api/sample/PathogenTestTypeTest.java

@@ -30,10 +30,8 @@ public class PathogenTestTypeTest {
 	 */
 	private static final Set<PathogenTestType> EXPECTED_LEGACY = EnumSet.of(
 		PathogenTestType.ANTIBODY_DETECTION,
-		PathogenTestType.ANTIGEN_DETECTION,
 		PathogenTestType.INCUBATION_TIME,
 		PathogenTestType.MICROSCOPY,
-		PathogenTestType.LATEX_AGGLUTINATION,
 		PathogenTestType.CQ_VALUE_DETECTION,
 		PathogenTestType.SEQUENCING,
 		// Superseded by the per-Ig-class ELISA split (#13951); kept so historic records still render and
@@ -100,7 +98,10 @@ public void newMethodsAreSelectable() {
 			PathogenTestType.MALDI_TOF,
 			PathogenTestType.ACID_FAST_STAIN,
 			PathogenTestType.GENOTYPIC_RESISTANCE_TEST,
-			PathogenTestType.FLOW_CYTOMETRY);
+			PathogenTestType.FLOW_CYTOMETRY,
+			PathogenTestType.ANTIGEN_DETECTION,
+			PathogenTestType.LATEX_AGGLUTINATION,
+			PathogenTestType.RSV_SUBTYPING);
 		for (PathogenTestType type : newlyAdded) {
 			assertTrue(PathogenTestType.isSelectableForNewTests(type), type.name() + " should be selectable for new tests");
 			assertFalse(EXPECTED_LEGACY.contains(type), type.name() + " is a new method, not legacy");

sormas-api/src/test/java/de/symeda/sormas/api/sample/SampleMaterialTest.java

@@ -22,8 +22,9 @@ public void testActiveMaterialsMatchUpgradedSpec() {
 
 		// Issue #13948 (#1): 44 from #13560 + 4 new (cord blood, lung tissue, placenta, ulcer swab)
 		// + 4 un-deprecated (biopsy, duodenum/intestinal fluid, lower respiratory tract)
-		// + oropharyngeal swab un-deprecated, throat swab now deprecated = 52 active specimen types
-		assertThat(active, hasSize(52));
+		// + oropharyngeal swab un-deprecated, throat swab now deprecated = 52
+		// + nasopharyngeal lavage re-activated for RSV (#14023) = 53 active specimen types
+		assertThat(active, hasSize(53));
 	}
 
 	@Test
@@ -37,7 +38,6 @@ public void testDeprecatedMaterials() {
 				SampleMaterial.URINE_PM,
 				SampleMaterial.CORNEA_PM,
 				SampleMaterial.NASAL_SWAB,
-				SampleMaterial.NASOPHARYNGEAL_LAVAGE,
 				SampleMaterial.THROAT_SWAB,
 				SampleMaterial.THROAT_ASPIRATE,
 				SampleMaterial.SOFT_TISSUE,

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

@@ -51,6 +51,8 @@ public static AbstractDiseaseSectionComponent forDisease(Disease disease) {
 			return new MalariaSectionComponent();
 		case SHIGELLOSIS:
 			return new ShigellosisSectionComponent();
+		case RESPIRATORY_SYNCYTIAL_VIRUS:
+			return new RsvSectionComponent();
 		default:
 			return new DefaultSectionComponent();
 		}

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

@@ -0,0 +1,86 @@
+/*******************************************************************************
+ * SORMAS® - Surveillance Outbreak Response Management & Analysis System
+ * Copyright © 2016-2018 Helmholtz-Zentrum für Infektionsforschung GmbH (HZI)
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *******************************************************************************/
+package de.symeda.sormas.ui.samples.diseasesection;
+
+import com.vaadin.ui.ComboBox;
+
+import de.symeda.sormas.api.sample.PathogenTestDto;
+import de.symeda.sormas.api.sample.PathogenTestResultType;
+import de.symeda.sormas.api.sample.PathogenTestType;
+import de.symeda.sormas.api.sample.RsvSubtype;
+import de.symeda.sormas.ui.samples.events.TestResultChangedEvent;
+import de.symeda.sormas.ui.samples.events.TestTypeChangedEvent;
+
+/**
+ * RSV section: reveals the RSV subtype (A or B) selector on a positive {@link PathogenTestType#RSV_SUBTYPING}
+ * result (#14024). The subtype is captured in {@link PathogenTestDto#getRsvSubtype()}.
+ */
+public class RsvSectionComponent extends AbstractDiseaseSectionComponent {
+
+	private ComboBox<RsvSubtype> rsvSubtypeField;
+
+	private PathogenTestType currentTestType;
+	private PathogenTestResultType currentResult;
+
+	@Override
+	protected void buildLayout() {
+		rsvSubtypeField = createComboBox(PathogenTestDto.RSV_SUBTYPE);
+		rsvSubtypeField.setItemCaptionGenerator(RsvSubtype::toString);
+		rsvSubtypeField.setVisible(false);
+		updateRsvSubtypeItems();
+		addRow(rsvSubtypeField);
+
+		binder.forField(rsvSubtypeField).bind(PathogenTestDto::getRsvSubtype, PathogenTestDto::setRsvSubtype);
+	}
+
+	@Override
+	protected void wireVisibility() {
+		track(eventBus.on(TestTypeChangedEvent.class, event -> {
+			currentTestType = event.getTestType();
+			updateVisibility();
+			updateRsvSubtypeItems();
+		}));
+
+		track(eventBus.on(TestResultChangedEvent.class, event -> {
+			currentResult = event.getTestResult();
+			updateVisibility();
+		}));
+	}
+
+	private void updateVisibility() {
+		boolean visible = currentTestType == PathogenTestType.RSV_SUBTYPING && currentResult == PathogenTestResultType.POSITIVE;
+		rsvSubtypeField.setVisible(visible);
+		if (!visible) {
+			rsvSubtypeField.clear();
+		}
+		updateRowAndSelfVisibility();
+	}
+
+	@Override
+	protected void clearOwnedFields() {
+		PathogenTestDto dto = binder.getBean();
+		if (dto == null) {
+			return;
+		}
+		dto.setRsvSubtype(null);
+	}
+
+	private void updateRsvSubtypeItems() {
+		updateComboBoxByDisease(rsvSubtypeField, RsvSubtype.class, disease);
+	}
+}