Merge pull request #13166 from SORMAS-Foundation/change-#13159-automatic-soft-delete-negative-covid-tests-and-samples

Change #13159 automatic soft delete negative covid tests and samples

Author: leventegal-she

sormas-api/src/main/java/de/symeda/sormas/api/ConfigFacade.java

@@ -161,4 +161,6 @@ public interface ConfigFacade {
 	CaseClassificationCalculationMode getCaseClassificationCalculationMode(Disease disease);
 
 	boolean isAnyCaseClassificationCalculationEnabled();
+
+	Integer getNegaiveCovidSamplesMaxAgeDays();
 }

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

@@ -21,4 +21,9 @@ public SampleReferenceDto getSample() {
 	public void setSample(SampleReferenceDto sample) {
 		this.sample = sample;
 	}
+
+	public PathogenTestCriteria sample(SampleReferenceDto sample) {
+		this.sample = sample;
+		return this;
+	}
 }

sormas-backend/src/main/java/de/symeda/sormas/backend/common/ConfigFacadeEjb.java

@@ -187,6 +187,7 @@ public class ConfigFacadeEjb implements ConfigFacade {
 	public static final int DEFAULT_DOCUMENT_UPLOAD_SIZE_LIMIT_MB = 20;
 	public static final String IMPORT_FILE_SIZE_LIMIT_MB = "importFileSizeLimitMb";
 	public static final int DEFAULT_IMPOR_FILE_SIZE_LIMIT_MB = 20;
+	public static final String NEGAIVE_COVID_SAMPLES_MAX_AGE_DAYS = "negaiveCovidSamplesMaxAgeDays";
 
 	private final Logger logger = LoggerFactory.getLogger(getClass());
 
@@ -838,6 +839,11 @@ public void resetRequestContext() {
 		RequestContextHolder.reset();
 	}
 
+	@Override
+	public Integer getNegaiveCovidSamplesMaxAgeDays() {
+		return parseProperty(NEGAIVE_COVID_SAMPLES_MAX_AGE_DAYS, null, Integer::parseInt);
+	}
+
 	@LocalBean
 	@Stateless
 	public static class ConfigFacadeEjbLocal extends ConfigFacadeEjb {

sormas-backend/src/main/java/de/symeda/sormas/backend/common/CronService.java

@@ -48,6 +48,7 @@
 import de.symeda.sormas.backend.immunization.ImmunizationFacadeEjb;
 import de.symeda.sormas.backend.infrastructure.central.CentralInfraSyncFacade;
 import de.symeda.sormas.backend.report.WeeklyReportFacadeEjb.WeeklyReportFacadeEjbLocal;
+import de.symeda.sormas.backend.sample.SampleService;
 import de.symeda.sormas.backend.specialcaseaccess.SpecialCaseAccessFacadeEjb.SpecialCaseAccessFacadeEjbLocal;
 import de.symeda.sormas.backend.systemevent.SystemEventFacadeEjb.SystemEventFacadeEjbLocal;
 import de.symeda.sormas.backend.task.TaskFacadeEjb.TaskFacadeEjbLocal;
@@ -96,6 +97,8 @@ public class CronService {
 	private SpecialCaseAccessFacadeEjbLocal specialCaseAccessFacade;
 	@EJB
 	private UserFacadeEjbLocal userFacade;
+	@EJB
+	private SampleService sampleService;
 
 	@Schedule(hour = "*", minute = "*/" + TASK_UPDATE_INTERVAL, second = "0", persistent = false)
 	public void sendNewAndDueTaskMessages() {
@@ -297,4 +300,9 @@ public void syncUsersFromAuthenticationProvider() {
 			userFacade.syncUsersFromAuthenticationProvider();
 		}
 	}
+
+	@Schedule(hour = "2", minute = "40", persistent = false)
+	public void sofDeleteOldNegativeSamples() {
+		sampleService.cleanupOldCovidSamples();
+	}
 }

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

@@ -248,7 +248,6 @@ public void setTestTypeText(String testTypeText) {
 	}
 
 	@Temporal(TemporalType.TIMESTAMP)
-	@Column(nullable = false)
 	public Date getTestDateTime() {
 		return testDateTime;
 	}

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

@@ -56,18 +56,23 @@
 
 import org.apache.commons.collections4.CollectionUtils;
 
+import de.symeda.sormas.api.Disease;
 import de.symeda.sormas.api.EntityRelevanceStatus;
 import de.symeda.sormas.api.RequestContextHolder;
 import de.symeda.sormas.api.caze.IsCase;
 import de.symeda.sormas.api.common.DeletableEntityType;
 import de.symeda.sormas.api.common.DeletionDetails;
+import de.symeda.sormas.api.common.DeletionReason;
 import de.symeda.sormas.api.common.progress.ProcessedEntity;
 import de.symeda.sormas.api.common.progress.ProcessedEntityStatus;
 import de.symeda.sormas.api.contact.ContactReferenceDto;
 import de.symeda.sormas.api.disease.DiseaseVariant;
 import de.symeda.sormas.api.event.EventParticipantReferenceDto;
 import de.symeda.sormas.api.feature.FeatureType;
+import de.symeda.sormas.api.i18n.I18nProperties;
+import de.symeda.sormas.api.i18n.Strings;
 import de.symeda.sormas.api.sample.IsSample;
+import de.symeda.sormas.api.sample.PathogenTestCriteria;
 import de.symeda.sormas.api.sample.PathogenTestResultType;
 import de.symeda.sormas.api.sample.PathogenTestType;
 import de.symeda.sormas.api.sample.SampleAssociationType;
@@ -87,6 +92,7 @@
 import de.symeda.sormas.backend.caze.CaseService;
 import de.symeda.sormas.backend.common.AbstractDeletableAdoService;
 import de.symeda.sormas.backend.common.AbstractDomainObject;
+import de.symeda.sormas.backend.common.ConfigFacadeEjb.ConfigFacadeEjbLocal;
 import de.symeda.sormas.backend.common.CriteriaBuilderHelper;
 import de.symeda.sormas.backend.common.DeletableAdo;
 import de.symeda.sormas.backend.common.JurisdictionFlagsService;
@@ -145,6 +151,8 @@ public class SampleService extends AbstractDeletableAdoService<Sample>
 	protected FeatureConfigurationFacadeEjbLocal featureConfigurationFacade;
 	@EJB
 	private SpecialCaseAccessService specialCaseAccessService;
+	@EJB
+	private ConfigFacadeEjbLocal configFacade;
 
 	public SampleService() {
 		super(Sample.class, DeletableEntityType.SAMPLE);
@@ -1276,4 +1284,37 @@ public List<DiseaseVariant> getAssociatedDiseaseVariants(String sampleUuid) {
 		cq.select(pathogenTestJoin.get(PathogenTest.TESTED_DISEASE_VARIANT));
 		return em.createQuery(cq).getResultList();
 	}
+
+	public void cleanupOldCovidSamples() {
+		final Integer maxAgeDays = configFacade.getNegaiveCovidSamplesMaxAgeDays();
+		if (maxAgeDays == null) {
+			return;
+		}
+
+		CriteriaBuilder cb = em.getCriteriaBuilder();
+		CriteriaQuery<PathogenTest> cq = cb.createQuery(PathogenTest.class);
+		Root<PathogenTest> from = cq.from(PathogenTest.class);
+
+		cq.where(
+			cb.equal(from.get(PathogenTest.TESTED_DISEASE), Disease.CORONAVIRUS),
+			cb.equal(from.get(PathogenTest.TEST_RESULT), PathogenTestResultType.NEGATIVE),
+			cb.notEqual(from.get(PathogenTest.DELETED), true),
+			cb.lessThan(
+				CriteriaBuilderHelper.coalesce(
+					cb,
+					Date.class,
+					from.get(PathogenTest.TEST_DATE_TIME),
+					from.get(PathogenTest.REPORT_DATE),
+					from.get(PathogenTest.CREATION_DATE)),
+				DateHelper.subtractDays(new Date(), maxAgeDays)));
+		em.createQuery(cq).getResultList().stream().collect(Collectors.groupingBy(PathogenTest::getSample)).forEach((sample, tests) -> {
+			if (pathogenTestService.count(new PathogenTestCriteria().sample(sample.toReference())) == tests.size()) {
+				delete(sample, new DeletionDetails(DeletionReason.OTHER_REASON, I18nProperties.getString(Strings.entityAutomaticSoftDeletion)));
+			} else {
+				tests.forEach(
+					p -> pathogenTestService
+						.delete(p, new DeletionDetails(DeletionReason.OTHER_REASON, I18nProperties.getString(Strings.entityAutomaticSoftDeletion))));
+			}
+		});
+	}
 }