Merge pull request #13577 from SORMAS-Foundation/bugfix-13548-dashboard-samples-error

Bugfix 13548 dashboard samples error

Author: KarnaiahPesula

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

@@ -15,13 +15,15 @@
 
 package de.symeda.sormas.api.dashboard;
 
+import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleMaterial;
 import de.symeda.sormas.api.sample.SampleDashboardFilterDateType;
 import de.symeda.sormas.api.sample.SampleMaterial;
 
 public class SampleDashboardCriteria extends BaseDashboardCriteria<SampleDashboardCriteria> {
 
 	private SampleDashboardFilterDateType sampleDateType;
 	private SampleMaterial sampleMaterial;
+	private EnvironmentSampleMaterial environmentSampleMaterial;
 
 	private Boolean withNoDisease;
 
@@ -56,6 +58,14 @@ public Boolean getWithNoDisease() {
 	public SampleDashboardCriteria withNoDisease(Boolean withNoDisease) {
 		this.withNoDisease = withNoDisease;
 
+		return self;
+	}
+	public EnvironmentSampleMaterial getEnvironmentSampleMaterial() {
+		return environmentSampleMaterial;
+	}
+	public SampleDashboardCriteria environmentSampleMaterial(EnvironmentSampleMaterial environmentSampleMaterial) {
+		this.environmentSampleMaterial = environmentSampleMaterial;
+
 		return self;
 	}
 }

sormas-api/src/main/java/de/symeda/sormas/api/dashboard/sample/SampleDashboardFacade.java

@@ -22,6 +22,7 @@
 import javax.ejb.Remote;
 
 import de.symeda.sormas.api.dashboard.SampleDashboardCriteria;
+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.SamplePurpose;
@@ -47,4 +48,12 @@ public interface SampleDashboardFacade {
 	List<MapSampleDto> getSamplesForMap(SampleDashboardCriteria criteria, Set<SampleAssociationType> associationTypes);
 
 	List<MapSampleDto> getEnvironmentalSamplesForMap(SampleDashboardCriteria criteria);
+
+	Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondition(SampleDashboardCriteria dashboardCriteria);
+
+	Map<SampleShipmentStatus, Long> getEnvironmentalSampleCountsByShipmentStatus(SampleDashboardCriteria dashboardCriteria);
+
+	Map<PathogenTestResultType, Long> getEnvironmentalTestResultCountsByResultType(SampleDashboardCriteria dashboardCriteria);
+
+	Map<EnvironmentSampleMaterial, Long> getEnvironmentalSampleCounts(SampleDashboardCriteria dashboardCriteria);
 }

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

@@ -141,6 +141,7 @@ public interface Descriptions {
 	String sampleDashboardCountsBySpecimenCondition = "sampleDashboardCountsBySpecimenCondition";
 	String sampleDashboardDiseaseFilter = "sampleDashboardDiseaseFilter";
 	String sampleDashboardDistrictFilter = "sampleDashboardDistrictFilter";
+	String sampleDashboardHumans = "sampleDashboardHumans";
 	String sampleDashboardRegionFilter = "sampleDashboardRegionFilter";
 	String SormasToSormasOptions_comment = "SormasToSormasOptions.comment";
 	String SurveillanceReport_associatedMessage = "SurveillanceReport.associatedMessage";

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

@@ -827,6 +827,7 @@ public interface Strings {
 	String headingSaveNotification = "headingSaveNotification";
 	String headingSaveUser = "headingSaveUser";
 	String headingSaveUserNotPossible = "headingSaveUserNotPossible";
+	String headingSearchSample = "headingSearchSample";
 	String headingSecurityAlert = "headingSecurityAlert";
 	String headingSeeAllPersons = "headingSeeAllPersons";
 	String headingSelectCampaign = "headingSelectCampaign";
@@ -1557,6 +1558,7 @@ public interface Strings {
 	String messageSampleOpened = "messageSampleOpened";
 	String messageSampleSaved = "messageSampleSaved";
 	String messageSamplesDeleted = "messageSamplesDeleted";
+	String messageSampleSearchWithDisease = "messageSampleSearchWithDisease";
 	String messageSamplesRestored = "messageSamplesRestored";
 	String messageSelectedPeriodTooLong = "messageSelectedPeriodTooLong";
 	String messageSelfReportArchived = "messageSelfReportArchived";

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

@@ -234,6 +234,7 @@ sampleDashboardDistrictFilter= The district of the associated Case/Contact/Event
 sampleDashboardDiseaseFilter= The disease of the associated Case/Contact/Event participant's event
 sampleDashboardCountsByShipmentStatus=Only samples with the purpose external lab testing are considered
 sampleDashboardCountsBySpecimenCondition=Only samples received and with the purpose external lab testing are considered
+sampleDashboardHumans=Only samples that are associated with human cases are taken into account
 
 aefiDashboardRegionFilter= The region of the associated immunization
 aefiDashboardDistrictFilter= The district of the associated immunization

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

@@ -516,6 +516,7 @@ headingCreateNewCaseIssue = Case creation issue
 headingCreateNewClinicalVisit = Create new clinical assessment
 headingCreateNewContact = Create new contact
 headingCreateNewContactIssue = Contact creation issue
+headingSearchSample = Sample search issue
 headingCreateNewTravelEntry=Create new travel entry
 headingCreateNewEnvironment = Create new environment
 headingCreateNewEvent = Create new event
@@ -1261,6 +1262,7 @@ messageEventParticipantsDeleted = All selected eligible event participants have
 messageEventParticipantResponsibleJurisdictionUpdated = Changing or removing the responsible jurisdiction of this event participant could make you lose access to its personal details and/or disallow you to edit it in the future. Are you sure you want to proceed?
 messageEventParticipantToCaseWithoutEventDisease=It is not possible to create cases from an event participant if the disease of the event has not been set
 messageEventParticipantToContactWithoutEventDisease=It is not possible to create a contact from an event participant if the disease of the event has not been set
+messageSampleSearchWithDisease=It is not possible to search for environment samples by disease.
 messageEventJurisdictionUpdated = Changing or removing the jurisdiction of this event could make you lose access to its personal details and/or disallow you to edit it in the future. Are you sure you want to proceed?
 messageEventSaved = Event data saved
 messageEventGroupSaved = Event group data saved

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

@@ -27,6 +27,7 @@
 import de.symeda.sormas.api.dashboard.sample.MapSampleDto;
 import de.symeda.sormas.api.dashboard.sample.SampleDashboardFacade;
 import de.symeda.sormas.api.dashboard.sample.SampleShipmentStatus;
+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.SamplePurpose;
@@ -73,7 +74,7 @@ public Long countSamplesForMap(SampleDashboardCriteria criteria, Set<SampleAssoc
 
 	@Override
 	public Long countEnvironmentalSamplesForMap(SampleDashboardCriteria criteria) {
-		return sampleDashboardService.countEnvironmentSamplesForMap(criteria);
+		return sampleDashboardService.countEnvironmentalSamplesForMap(criteria);
 	}
 
 	@Override
@@ -86,6 +87,26 @@ public List<MapSampleDto> getEnvironmentalSamplesForMap(SampleDashboardCriteria
 		return sampleDashboardService.getEnvironmentalSamplesForMap(criteria);
 	}
 
+	@Override
+	public Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondition(SampleDashboardCriteria dashboardCriteria) {
+		return sampleDashboardService.getEnvironmentalSampleCountsBySpecimenCondition(dashboardCriteria);
+	}
+
+	@Override
+	public Map<SampleShipmentStatus, Long> getEnvironmentalSampleCountsByShipmentStatus(SampleDashboardCriteria dashboardCriteria) {
+		return sampleDashboardService.getEnvironmentalSampleCountsByShipmentStatus(dashboardCriteria);
+	}
+
+	@Override
+	public Map<PathogenTestResultType, Long> getEnvironmentalTestResultCountsByResultType(SampleDashboardCriteria dashboardCriteria) {
+		return sampleDashboardService.getEnvironmentalTestResultCountsByResultType(dashboardCriteria);
+	}
+
+	@Override
+	public Map<EnvironmentSampleMaterial, Long> getEnvironmentalSampleCounts(SampleDashboardCriteria dashboardCriteria) {
+		return sampleDashboardService.getEnvironmentalSampleCounts(dashboardCriteria);
+	}
+
 	@LocalBean
 	@Stateless
 	public static class SampleDashboardFacadeEjbLocal extends SampleDashboardFacadeEjb {

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

@@ -45,6 +45,7 @@
 import javax.persistence.criteria.Selection;
 import javax.persistence.criteria.Subquery;
 
+import de.symeda.sormas.api.environment.environmentsample.EnvironmentSampleMaterial;
 import org.apache.commons.lang3.tuple.Pair;
 import org.jetbrains.annotations.NotNull;
 
@@ -147,6 +148,36 @@ public Map<SpecimenCondition, Long> getSampleCountsBySpecimenCondition(SampleDas
 			(cb, root) -> cb.and(buildExternalSamplePredicate(cb, root), cb.equal(root.get(Sample.RECEIVED), true)));
 	}
 
+	public Map<SpecimenCondition, Long> getEnvironmentalSampleCountsBySpecimenCondition(SampleDashboardCriteria dashboardCriteria) {
+		return getEnvironmentalSampleCountsBySpecimenCondition(
+				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) {
+		final CriteriaBuilder cb = em.getCriteriaBuilder();
+		final CriteriaQuery<Tuple> cq = cb.createTupleQuery();
+		final Root<EnvironmentSample> sample = cq.from(EnvironmentSample.class);
+		EnvironmentSampleJoins joins = new EnvironmentSampleJoins(sample);
+		final Path<Object> groupingProperty = sample.get(property);
+
+		cq.multiselect(groupingProperty, cb.count(sample));
+
+		final Predicate criteriaFilter = createEnvironmentSampleFilter(new EnvironmentSampleQueryContext(cb, cq, sample, joins), dashboardCriteria);
+		cq.where(CriteriaBuilderHelper.and(cb, criteriaFilter, additionalFilters != null ? additionalFilters.apply(cb, sample) : null));
+
+		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)));
+	}
+
 	private <T extends Enum<?>> Map<T, Long> getSampleCountsByEnumProperty(
 		String property,
 		Class<T> propertyType,
@@ -188,8 +219,27 @@ 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) {
+		final CriteriaBuilder cb = em.getCriteriaBuilder();
+		final CriteriaQuery<Tuple> cq = cb.createTupleQuery();
+		final Root<EnvironmentSample> sample = cq.from(EnvironmentSample.class);
+		EnvironmentSampleJoins joins = new EnvironmentSampleJoins(sample);
+		Path<Boolean> shipped = sample.get(EnvironmentSample.DISPATCHED);
+		Path<Boolean> received = sample.get(EnvironmentSample.RECEIVED);
+		cq.multiselect(shipped, received, cb.count(sample));
+
+		final Predicate criteriaFilter = createEnvironmentSampleFilter(new EnvironmentSampleQueryContext(cb, cq, sample, joins), dashboardCriteria);
+		cq.where(criteriaFilter);
+
+		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));
 	}
 
 	private SampleShipmentStatus getSampleShipmentStatusByFlags(Boolean shipped, Boolean received) {
@@ -215,6 +265,54 @@ public Map<PathogenTestResultType, Long> getTestResultCountsByResultType(SampleD
 			.collect(Collectors.toMap(t -> (PathogenTestResultType) t.get(0), t -> (Long) t.get(1)));
 	}
 
+	/**
+	 * Returns a map of counts of environment samples by result type.
+	 *
+	 * @param dashboardCriteria
+	 * @return
+	 */
+	public Map<PathogenTestResultType, Long> getEnvironmentalTestResultCountsByResultType(SampleDashboardCriteria dashboardCriteria) {
+		final CriteriaBuilder cb = em.getCriteriaBuilder();
+		final CriteriaQuery<Tuple> cq = cb.createTupleQuery();
+		final Root<EnvironmentSample> sample = cq.from(EnvironmentSample.class);
+		Join<EnvironmentSample, PathogenTest> pathogenTestJoin = sample.join(EnvironmentSample.PATHOGEN_TESTS, JoinType.LEFT);
+		final Path<Object> pathogenTestResult = pathogenTestJoin.get(PathogenTest.TEST_RESULT);
+		EnvironmentSampleJoins joins = new EnvironmentSampleJoins(sample);
+		cq.multiselect(pathogenTestResult, cb.count(pathogenTestJoin));
+
+		final Predicate criteriaFilter = createEnvironmentSampleFilter(new EnvironmentSampleQueryContext(cb, cq, sample, joins), dashboardCriteria);
+		cq.where(criteriaFilter);
+
+		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)));
+	}
+
+	/**
+	 * Returns a map of counts of environment samples by material type.
+	 *
+	 * @param dashboardCriteria
+	 * @return
+	 */
+	public Map<EnvironmentSampleMaterial, Long> getEnvironmentalSampleCounts(SampleDashboardCriteria dashboardCriteria) {
+		// This method is used to get the counts of environment samples by material type
+		final CriteriaBuilder cb = em.getCriteriaBuilder();
+		final CriteriaQuery<Tuple> cq = cb.createTupleQuery();
+		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);
+		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)));
+	}
+
 	private static <J extends ISampleJoins> List<Selection<?>> getCoordinatesSelection(
 		SampleAssociationType associationType,
 		J joins,
@@ -287,7 +385,7 @@ public Long countSamplesForMap(SampleDashboardCriteria criteria, Set<SampleAssoc
 		return QueryHelper.getSingleResult(em, cq);
 	}
 
-	public Long countEnvironmentSamplesForMap(SampleDashboardCriteria criteria) {
+	public Long countEnvironmentalSamplesForMap(SampleDashboardCriteria criteria) {
 		final CriteriaBuilder cb = em.getCriteriaBuilder();
 		final CriteriaQuery<Long> cq = cb.createQuery(Long.class);
 		final Root<EnvironmentSample> sample = cq.from(EnvironmentSample.class);
@@ -474,8 +572,8 @@ private Predicate createEnvironmentSampleFilter(EnvironmentSampleQueryContext qu
 			filter = CriteriaBuilderHelper.and(cb, filter, dateFilter);
 		}
 
-		if (criteria.getSampleMaterial() != null) {
-			filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(sampleRoot.get(EnvironmentSample.SAMPLE_MATERIAL), criteria.getSampleMaterial()));
+		if (criteria.getEnvironmentSampleMaterial() != null) {
+			filter = CriteriaBuilderHelper.and(cb, filter, cb.equal(sampleRoot.get(EnvironmentSample.SAMPLE_MATERIAL), criteria.getEnvironmentSampleMaterial()));
 		}
 
 		return CriteriaBuilderHelper.and(

sormas-ui/src/main/java/de/symeda/sormas/ui/dashboard/diagram/AbstractEpiCurveComponent.java

@@ -22,6 +22,8 @@
 import java.util.List;
 import java.util.function.Consumer;
 
+import com.vaadin.shared.ui.ContentMode;
+import com.vaadin.ui.Component;
 import org.vaadin.hene.popupbutton.PopupButton;
 
 import com.vaadin.icons.VaadinIcons;
@@ -51,11 +53,14 @@ public abstract class AbstractEpiCurveComponent<P extends AbstractDashboardDataP
 	protected final P dashboardDataProvider;
 	protected final HighChart epiCurveChart;
 	protected Label epiCurveLabel;
+	protected Label infoIcon;
 
 	// Others
 	protected EpiCurveGrouping epiCurveGrouping;
 	private boolean showMinimumEntries;
 	private Consumer<Boolean> externalExpandListener;
+	private HorizontalLayout epiCurveHeaderLayout;
+	private Button expandEpiCurveButton;
 
 	public AbstractEpiCurveComponent(P dashboardDataProvider) {
 
@@ -79,13 +84,36 @@ public AbstractEpiCurveComponent(P dashboardDataProvider) {
 		//clearAndFillEpiCurveChart();
 	}
 
+	public AbstractEpiCurveComponent(P dashboardDataProvider, String description) {
+		this(dashboardDataProvider);
+
+		infoIcon = new Label(VaadinIcons.INFO_CIRCLE.getHtml(), ContentMode.HTML);
+		CssStyles.style(infoIcon, CssStyles.H3, CssStyles.VSPACE_4, CssStyles.VSPACE_TOP_NONE, CssStyles.HSPACE_LEFT_4);
+
+		this.infoIcon.setDescription(I18nProperties.getDescription(description));
+		epiCurveLabel.setSizeUndefined();
+		CssStyles.style(epiCurveLabel, CssStyles.H2, CssStyles.VSPACE_4, CssStyles.VSPACE_TOP_NONE);
+		HorizontalLayout labelWithInfoLayout = new HorizontalLayout(epiCurveLabel, infoIcon);
+		labelWithInfoLayout.setMargin(false);
+		labelWithInfoLayout.setSpacing(false);
+		// Replace the original epiCurveLabel with the new one that includes the info icon
+		// in the header layout
+		epiCurveHeaderLayout.removeComponent(epiCurveLabel);
+		epiCurveHeaderLayout.removeComponent(expandEpiCurveButton);
+		epiCurveHeaderLayout.addComponent(labelWithInfoLayout);
+		epiCurveHeaderLayout.setComponentAlignment(labelWithInfoLayout, Alignment.BOTTOM_LEFT);
+		epiCurveHeaderLayout.setExpandRatio(labelWithInfoLayout, 1f);
+		epiCurveHeaderLayout.addComponent(expandEpiCurveButton);
+		epiCurveHeaderLayout.setComponentAlignment(expandEpiCurveButton, Alignment.TOP_RIGHT);
+	}
+
 	public void setExpandListener(Consumer<Boolean> listener) {
 		externalExpandListener = listener;
 	}
 
 	private HorizontalLayout createHeader() {
 
-		HorizontalLayout epiCurveHeaderLayout = new HorizontalLayout();
+		epiCurveHeaderLayout = new HorizontalLayout();
 		epiCurveHeaderLayout.setWidth(100, Unit.PERCENTAGE);
 		epiCurveHeaderLayout.setSpacing(true);
 		CssStyles.style(epiCurveHeaderLayout, CssStyles.VSPACE_4);
@@ -99,7 +127,7 @@ private HorizontalLayout createHeader() {
 		epiCurveHeaderLayout.setExpandRatio(epiCurveLabel, 1);
 
 		// "Expand" and "Collapse" buttons
-		Button expandEpiCurveButton =
+		expandEpiCurveButton =
 			ButtonHelper.createIconButtonWithCaption("expandEpiCurve", "", VaadinIcons.EXPAND, null, CssStyles.BUTTON_SUBTLE, CssStyles.VSPACE_NONE);
 		Button collapseEpiCurveButton = ButtonHelper
 			.createIconButtonWithCaption("collapseEpiCurve", "", VaadinIcons.COMPRESS, null, CssStyles.BUTTON_SUBTLE, CssStyles.VSPACE_NONE);