Filter cases and the sample dashboard by pathogen test result, serogr…

sormas-api/src/main/java/de/symeda/sormas/api/caze/CaseCriteria.java

@@ -35,6 +35,7 @@
 import de.symeda.sormas.api.person.PersonReferenceDto;
 import de.symeda.sormas.api.person.PresentCondition;
 import de.symeda.sormas.api.person.SymptomJournalStatus;
+import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.share.ExternalShareCriteria;
 import de.symeda.sormas.api.survey.SurveyReferenceDto;
 import de.symeda.sormas.api.user.UserReferenceDto;
@@ -92,10 +93,14 @@ public class CaseCriteria extends CriteriaWithDateType implements ExternalShareC
 	public static final String SURVEY_ASSIGNED_TO = "surveyAssignedTo";
 	public static final String SURVEY_RESPONSE_STATUS = "surveyResponseStatus";
 	public static final String SURVEY = "survey";
+	public static final String PATHOGEN_TEST_RESULT = "pathogenTestResult";
+	public static final String SEROGROUP = "serogroup";
 
 	private UserRoleReferenceDto reportingUserRole;
 	private Disease disease;
 	private DiseaseVariant diseaseVariant;
+	private PathogenTestResultType pathogenTestResult;
+	private String serogroup;
 	private CaseOutcome outcome;
 	private CaseClassification caseClassification;
 	private InvestigationStatus investigationStatus;
@@ -235,6 +240,33 @@ public DiseaseVariant getDiseaseVariant() {
 		return diseaseVariant;
 	}
 
+	public void setPathogenTestResult(PathogenTestResultType pathogenTestResult) {
+		this.pathogenTestResult = pathogenTestResult;
+	}
+
+	public CaseCriteria pathogenTestResult(PathogenTestResultType pathogenTestResult) {
+		setPathogenTestResult(pathogenTestResult);
+		return this;
+	}
+
+	public PathogenTestResultType getPathogenTestResult() {
+		return pathogenTestResult;
+	}
+
+	public void setSerogroup(String serogroup) {
+		this.serogroup = serogroup;
+	}
+
+	public CaseCriteria serogroup(String serogroup) {
+		setSerogroup(serogroup);
+		return this;
+	}
+
+	@IgnoreForUrl
+	public String getSerogroup() {
+		return serogroup;
+	}
+
 	public void setJurisdictionType(CaseJurisdictionType jurisdictionType) {
 		this.jurisdictionType = jurisdictionType;
 	}

sormas-api/src/main/java/de/symeda/sormas/api/dashboard/SampleDashboardCriteria.java

@@ -15,7 +15,9 @@
 
 package de.symeda.sormas.api.dashboard;
 
+import de.symeda.sormas.api.disease.DiseaseVariant;
 import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleMaterial;
+import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.SampleDashboardFilterDateType;
 import de.symeda.sormas.api.sample.SampleMaterial;
 
@@ -24,6 +26,9 @@ public class SampleDashboardCriteria extends BaseDashboardCriteria<SampleDashboa
 	private SampleDashboardFilterDateType sampleDateType;
 	private SampleMaterial sampleMaterial;
 	private EnvironmentSampleMaterial environmentSampleMaterial;
+	private PathogenTestResultType pathogenTestResult;
+	private String serogroup;
+	private DiseaseVariant diseaseVariant;
 
 	private Boolean withNoDisease;
 
@@ -60,12 +65,44 @@ public SampleDashboardCriteria withNoDisease(Boolean withNoDisease) {
 
 		return self;
 	}
+
 	public EnvironmentSampleMaterial getEnvironmentSampleMaterial() {
 		return environmentSampleMaterial;
 	}
+
 	public SampleDashboardCriteria environmentSampleMaterial(EnvironmentSampleMaterial environmentSampleMaterial) {
 		this.environmentSampleMaterial = environmentSampleMaterial;
 
 		return self;
 	}
+
+	public PathogenTestResultType getPathogenTestResult() {
+		return pathogenTestResult;
+	}
+
+	public SampleDashboardCriteria pathogenTestResult(PathogenTestResultType pathogenTestResult) {
+		this.pathogenTestResult = pathogenTestResult;
+
+		return self;
+	}
+
+	public String getSerogroup() {
+		return serogroup;
+	}
+
+	public SampleDashboardCriteria serogroup(String serogroup) {
+		this.serogroup = serogroup;
+
+		return self;
+	}
+
+	public DiseaseVariant getDiseaseVariant() {
+		return diseaseVariant;
+	}
+
+	public SampleDashboardCriteria diseaseVariant(DiseaseVariant diseaseVariant) {
+		this.diseaseVariant = diseaseVariant;
+
+		return self;
+	}
 }

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

@@ -2893,6 +2893,7 @@ public interface Captions {
 	String selfReportDeletedEnvironments = "selfReportDeletedEnvironments";
 	String selfReportProcess = "selfReportProcess";
 	String selfReportSelfReportsList = "selfReportSelfReportsList";
+	String serogroup = "serogroup";
 	String sex = "sex";
 	String showPlacesOnMap = "showPlacesOnMap";
 	String singleDayEventDate = "singleDayEventDate";

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

@@ -32,6 +32,7 @@ epiWeekTo=To Epi Week
 facilityType=Facility type
 facilityTypeGroup=Facility category
 featureConfiguration=Feature Configuration
+serogroup=Serogroup
 firstName=First name
 sex=Sex
 nationalHealthId=National health ID

sormas-backend/src/main/java/de/symeda/sormas/backend/caze/CaseService.java

@@ -158,6 +158,7 @@
 import de.symeda.sormas.backend.location.Location;
 import de.symeda.sormas.backend.person.Person;
 import de.symeda.sormas.backend.person.PersonQueryContext;
+import de.symeda.sormas.backend.sample.PathogenTest;
 import de.symeda.sormas.backend.sample.Sample;
 import de.symeda.sormas.backend.sample.SampleJoins;
 import de.symeda.sormas.backend.sample.SampleService;
@@ -706,6 +707,28 @@ public <T extends AbstractDomainObject> Predicate createCriteriaFilter(CaseCrite
 			filter =
 				CriteriaBuilderHelper.and(cb, filter, cb.equal(from.get(Case.DISEASE_VARIANT_VALUE), caseCriteria.getDiseaseVariant().getValue()));
 		}
+		if (caseCriteria.getPathogenTestResult() != null) {
+			Subquery<Long> resultSubquery = cq.subquery(Long.class);
+			Root<Sample> sampleRoot = resultSubquery.from(Sample.class);
+			resultSubquery.select(sampleRoot.get(AbstractDomainObject.ID));
+			resultSubquery.where(
+				cb.equal(sampleRoot.get(Sample.ASSOCIATED_CASE), from),
+				cb.equal(sampleRoot.get(Sample.PATHOGEN_TEST_RESULT), caseCriteria.getPathogenTestResult()),
+				cb.isFalse(sampleRoot.get(DeletableAdo.DELETED)));
+			filter = CriteriaBuilderHelper.and(cb, filter, cb.exists(resultSubquery));
+		}
+		if (StringUtils.isNotBlank(caseCriteria.getSerogroup())) {
+			Subquery<Long> serogroupSubquery = cq.subquery(Long.class);
+			Root<Sample> sampleRoot = serogroupSubquery.from(Sample.class);
+			Join<Sample, PathogenTest> pathogenTestJoin = sampleRoot.join(Sample.PATHOGENTESTS, JoinType.INNER);
+			serogroupSubquery.select(sampleRoot.get(AbstractDomainObject.ID));
+			serogroupSubquery.where(
+				cb.equal(sampleRoot.get(Sample.ASSOCIATED_CASE), from),
+				CriteriaBuilderHelper.unaccentedIlike(cb, pathogenTestJoin.get(PathogenTest.SEROTYPE_TEXT), caseCriteria.getSerogroup().trim()),
+				cb.isFalse(sampleRoot.get(DeletableAdo.DELETED)),
+				cb.isFalse(pathogenTestJoin.get(DeletableAdo.DELETED)));
+			filter = CriteriaBuilderHelper.and(cb, filter, cb.exists(serogroupSubquery));
+		}
 		if (caseCriteria.getOutcome() != null) {
 			filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(from.get(Case.OUTCOME), caseCriteria.getOutcome()));
 		}
@@ -2045,7 +2068,7 @@ private Predicate getSimilarityFilters(CaseSimilarityCriteria criteria, Criteria
 
 	/**
 	 * Performance: May be slow when there are 10000s of cases with similar report date in the same region.
-	 * 
+	 *
 	 * @param limit
 	 *            null: no limit
 	 */
@@ -2338,7 +2361,7 @@ private List<Case> getCasesSetAsDuplicate(Long caseId) {
 	/**
 	 * Updates the vaccination status of all cases of the specified person and disease using
 	 * vaccination status data derived from immunization records.
-	 * 
+	 *
 	 * @param personId
 	 *            The ID of the case person whose cases should be updated
 	 * @param disease
@@ -2352,7 +2375,7 @@ public void updateVaccinationStatuses(Long personId, Disease disease, Vaccinatio
 
 	/**
 	 * Updates vaccination statuses using the enhanced determination logic (determined mode).
-	 * 
+	 *
 	 * <p>
 	 * This method updates cases with sophisticated vaccination statuses derived from immunization data.
 	 * It uses {@link ImmunizationService#deriveVaccinationStatus} to compute statuses that reflect:
@@ -2363,12 +2386,12 @@ public void updateVaccinationStatuses(Long personId, Disease disease, Vaccinatio
 	 * <li>Other immunity sources (OTHER status)</li>
 	 * <li>Immunization validity periods (validFrom/validUntil dates)</li>
 	 * </ul>
-	 * 
+	 *
 	 * <p>
 	 * The method only updates cases where the derived status differs from the current status,
 	 * and automatically updates the change date timestamp.
 	 * </p>
-	 * 
+	 *
 	 * @param personId
 	 *            The ID of the person whose cases should be updated
 	 * @param disease

sormas-backend/src/main/java/de/symeda/sormas/backend/dashboard/sample/SampleDashboardService.java

@@ -45,14 +45,15 @@
 import javax.persistence.criteria.Selection;
 import javax.persistence.criteria.Subquery;
 
-import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleMaterial;
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.jetbrains.annotations.NotNull;
 
 import de.symeda.sormas.api.dashboard.SampleDashboardCriteria;
 import de.symeda.sormas.api.dashboard.sample.MapSampleDto;
 import de.symeda.sormas.api.dashboard.sample.SampleShipmentStatus;
 import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleCriteria;
+import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleMaterial;
 import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.SampleAssociationType;
 import de.symeda.sormas.api.sample.SampleCriteria;
@@ -150,15 +151,17 @@ public Map<SpecimenCondition, Long> getSampleCountsBySpecimenCondition(SampleDas
 
 	public Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondition(SampleDashboardCriteria dashboardCriteria) {
 		return getEnvironmentalSampleCountsBySpecimenCondition(
-				EnvironmentSample.SPECIMEN_CONDITION,
-				SpecimenCondition.class,
-				dashboardCriteria,
-				null);
+			EnvironmentSample.SPECIMEN_CONDITION,
+			SpecimenCondition.class,
+			dashboardCriteria,
+			null);
 	}
 
-	private Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondition(String property, Class<SpecimenCondition> propertyType,
-																					   SampleDashboardCriteria dashboardCriteria,
-																					   BiFunction<CriteriaBuilder, Root<EnvironmentSample>, Predicate> additionalFilters) {
+	private Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondition(
+		String property,
+		Class<SpecimenCondition> propertyType,
+		SampleDashboardCriteria dashboardCriteria,
+		BiFunction<CriteriaBuilder, Root<EnvironmentSample>, Predicate> additionalFilters) {
 		final CriteriaBuilder cb = em.getCriteriaBuilder();
 		final CriteriaQuery<Tuple> cq = cb.createTupleQuery();
 		final Root<EnvironmentSample> sample = cq.from(EnvironmentSample.class);
@@ -173,9 +176,9 @@ private Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondi
 		cq.groupBy(groupingProperty);
 
 		return QueryHelper.getResultList(em, cq, null, null, Function.identity())
-				.stream()
-				.filter(t -> t.get(0) != null)
-				.collect(Collectors.toMap(t -> propertyType.cast(t.get(0)), t -> (Long) t.get(1)));
+			.stream()
+			.filter(t -> t.get(0) != null)
+			.collect(Collectors.toMap(t -> propertyType.cast(t.get(0)), t -> (Long) t.get(1)));
 	}
 
 	private <T extends Enum<?>> Map<T, Long> getSampleCountsByEnumProperty(
@@ -219,8 +222,8 @@ public Map<SampleShipmentStatus, Long> getSampleCountsByShipmentStatus(SampleDas
 		cq.groupBy(shipped, received);
 
 		return QueryHelper.getResultList(em, cq, null, null, Function.identity())
-				.stream()
-				.collect(Collectors.toMap(t -> getSampleShipmentStatusByFlags((Boolean) t.get(0), (Boolean) t.get(1)), t -> (Long) t.get(2), Long::sum));
+			.stream()
+			.collect(Collectors.toMap(t -> getSampleShipmentStatusByFlags((Boolean) t.get(0), (Boolean) t.get(1)), t -> (Long) t.get(2), Long::sum));
 	}
 
 	public Map<SampleShipmentStatus, Long> getEnvironmentalSampleCountsByShipmentStatus(SampleDashboardCriteria dashboardCriteria) {
@@ -238,8 +241,8 @@ public Map<SampleShipmentStatus, Long> getEnvironmentalSampleCountsByShipmentSta
 		cq.groupBy(shipped, received);
 
 		return QueryHelper.getResultList(em, cq, null, null, Function.identity())
-				.stream()
-				.collect(Collectors.toMap(t -> getSampleShipmentStatusByFlags((Boolean) t.get(0), (Boolean) t.get(1)), t -> (Long) t.get(2), Long::sum));
+			.stream()
+			.collect(Collectors.toMap(t -> getSampleShipmentStatusByFlags((Boolean) t.get(0), (Boolean) t.get(1)), t -> (Long) t.get(2), Long::sum));
 	}
 
 	private SampleShipmentStatus getSampleShipmentStatusByFlags(Boolean shipped, Boolean received) {
@@ -255,7 +258,10 @@ public Map<PathogenTestResultType, Long> getTestResultCountsByResultType(SampleD
 
 		cq.multiselect(pathogenTestResult, cb.count(pathogenTestJoin));
 
-		final Predicate criteriaFilter = createSampleFilter(new SampleQueryContext(cb, cq, sample), dashboardCriteria);
+		Predicate criteriaFilter = createSampleFilter(new SampleQueryContext(cb, cq, sample), dashboardCriteria);
+		if (dashboardCriteria.getPathogenTestResult() != null) {
+			criteriaFilter = CriteriaBuilderHelper.and(cb, criteriaFilter, cb.equal(pathogenTestResult, dashboardCriteria.getPathogenTestResult()));
+		}
 		cq.where(criteriaFilter);
 
 		cq.groupBy(pathogenTestResult);
@@ -286,9 +292,9 @@ public Map<PathogenTestResultType, Long> getEnvironmentalTestResultCountsByResul
 		cq.groupBy(pathogenTestResult);
 
 		return QueryHelper.getResultList(em, cq, null, null, Function.identity())
-				.stream()
-				.filter(t -> t.get(0) != null)
-				.collect(Collectors.toMap(t -> (PathogenTestResultType) t.get(0), t -> (Long) t.get(1)));
+			.stream()
+			.filter(t -> t.get(0) != null)
+			.collect(Collectors.toMap(t -> (PathogenTestResultType) t.get(0), t -> (Long) t.get(1)));
 	}
 
 	/**
@@ -304,13 +310,14 @@ public Map<EnvironmentSampleMaterial, Long> getEnvironmentalSampleCounts(SampleD
 		final Root<EnvironmentSample> sample = cq.from(EnvironmentSample.class);
 		final Path<Object> groupingProperty = sample.get(EnvironmentSample.SAMPLE_MATERIAL);
 		cq.multiselect(groupingProperty, cb.count(sample));
-		final Predicate criteriaFilter = createEnvironmentSampleFilter(new EnvironmentSampleQueryContext(cb, cq, sample, new EnvironmentSampleJoins(sample)), dashboardCriteria);
+		final Predicate criteriaFilter =
+			createEnvironmentSampleFilter(new EnvironmentSampleQueryContext(cb, cq, sample, new EnvironmentSampleJoins(sample)), dashboardCriteria);
 		cq.where(criteriaFilter);
 		cq.groupBy(groupingProperty);
 		return QueryHelper.getResultList(em, cq, null, null, Function.identity())
-				.stream()
-				.filter(t -> t.get(0) != null)
-				.collect(Collectors.toMap(t -> (EnvironmentSampleMaterial) t.get(0), t -> (Long) t.get(1)));
+			.stream()
+			.filter(t -> t.get(0) != null)
+			.collect(Collectors.toMap(t -> (EnvironmentSampleMaterial) t.get(0), t -> (Long) t.get(1)));
 	}
 
 	private static <J extends ISampleJoins> List<Selection<?>> getCoordinatesSelection(
@@ -510,6 +517,32 @@ private <T extends AbstractDomainObject> Predicate createSampleFilter(SampleQuer
 			filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(sampleRoot.get(Sample.SAMPLE_MATERIAL), criteria.getSampleMaterial()));
 		}
 
+		// Test result is denormalized on the sample (final lab result) → direct equality, no join.
+		if (criteria.getPathogenTestResult() != null) {
+			filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(sampleRoot.get(Sample.PATHOGEN_TEST_RESULT), criteria.getPathogenTestResult()));
+		}
+
+		if (StringUtils.isNotBlank(criteria.getSerogroup())) {
+			Subquery<Long> serogroupSubquery = cq.subquery(Long.class);
+			Root<PathogenTest> pathogenTestRoot = serogroupSubquery.from(PathogenTest.class);
+			serogroupSubquery.select(pathogenTestRoot.get(PathogenTest.ID));
+			serogroupSubquery.where(
+				cb.equal(pathogenTestRoot.get(PathogenTest.SAMPLE), sampleRoot),
+				CriteriaBuilderHelper.unaccentedIlike(cb, pathogenTestRoot.get(PathogenTest.SEROTYPE_TEXT), criteria.getSerogroup().trim()),
+				cb.isFalse(pathogenTestRoot.get(PathogenTest.DELETED)));
+			filter = CriteriaBuilderHelper.and(cb, filter, cb.exists(serogroupSubquery));
+		}
+		if (criteria.getDiseaseVariant() != null) {
+			Subquery<Long> variantSubquery = cq.subquery(Long.class);
+			Root<PathogenTest> pathogenTestRoot = variantSubquery.from(PathogenTest.class);
+			variantSubquery.select(pathogenTestRoot.get(PathogenTest.ID));
+			variantSubquery.where(
+				cb.equal(pathogenTestRoot.get(PathogenTest.SAMPLE), sampleRoot),
+				cb.equal(pathogenTestRoot.get(PathogenTest.TESTED_DISEASE_VARIANT_VALUE), criteria.getDiseaseVariant().getValue()),
+				cb.isFalse(pathogenTestRoot.get(PathogenTest.DELETED)));
+			filter = CriteriaBuilderHelper.and(cb, filter, cb.exists(variantSubquery));
+		}
+
 		if (Boolean.TRUE.equals(criteria.getWithNoDisease())) {
 			filter = CriteriaBuilderHelper.and(cb, filter, cb.isNotNull(joins.getEventParticipant()), cb.isNull(joins.getEvent().get(Event.DISEASE)));
 		} else if (Boolean.FALSE.equals(criteria.getWithNoDisease())) {
@@ -573,7 +606,8 @@ private Predicate createEnvironmentSampleFilter(EnvironmentSampleQueryContext qu
 		}
 
 		if (criteria.getEnvironmentSampleMaterial() != null) {
-			filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(sampleRoot.get(EnvironmentSample.SAMPLE_MATERIAL), criteria.getEnvironmentSampleMaterial()));
+			filter = CriteriaBuilderHelper
+				.and(cb, filter, cb.equal(sampleRoot.get(EnvironmentSample.SAMPLE_MATERIAL), criteria.getEnvironmentSampleMaterial()));
 		}
 
 		return CriteriaBuilderHelper.and(

sormas-backend/src/main/java/de/symeda/sormas/backend/sample/PathogenTest.java

@@ -89,6 +89,7 @@ public class PathogenTest extends DeletableAdo {
 	public static final String TEST_RESULT_VERIFIED = "testResultVerified";
 	public static final String FOUR_FOLD_INCREASE_ANTIBODY_TITER = "fourFoldIncreaseAntibodyTiter";
 	public static final String SEROTYPE = "serotype";
+	public static final String SEROTYPE_TEXT = "serotypeText";
 	public static final String CQ_VALUE = "cqValue";
 	public static final String CT_VALUE_E = "ctValueE";
 	public static final String CT_VALUE_N = "ctValueN";