Merge pull request #13161 from SORMAS-Foundation/change-#13154-automatic-processing-new-case-if-there-is-a-too-old-one

#13154 [Automatic lab message processing] Create new case if the exis…

Author: leventegal-she

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

@@ -2334,13 +2334,7 @@ protected String getDeleteReferenceField(DeletionReference deletionReference) {
 		return super.getDeleteReferenceField(deletionReference);
 	}
 
-	public String getCaseUuidForAutomaticSampleAssignment(Set<String> uuids, Disease disease) {
-		Integer automaticSampleAssignmentThreshold = diseaseConfigurationFacade.getAutomaticSampleAssignmentThreshold(disease);
-
-		if (automaticSampleAssignmentThreshold == null) {
-			return null;
-		}
-
+	public String getCaseUuidForAutomaticSampleAssignment(Set<String> uuids, Disease disease, int threshold) {
 		CriteriaBuilder cb = em.getCriteriaBuilder();
 		CriteriaQuery<String> cq = cb.createQuery(String.class);
 		Root<Case> caseRoot = cq.from(Case.class);
@@ -2362,9 +2356,10 @@ public String getCaseUuidForAutomaticSampleAssignment(Set<String> uuids, Disease
 						Date.class,
 						CriteriaBuilderHelper.coalesce(cb, Date.class, earliestSampleSq, caseRoot.get(Case.REPORT_DATE))),
 					cb.function(ExtendedPostgreSQL94Dialect.DATE, Date.class, cb.literal(new Date()))),
-				Long.valueOf(TimeUnit.DAYS.toSeconds(automaticSampleAssignmentThreshold)).doubleValue()));
+				Long.valueOf(TimeUnit.DAYS.toSeconds(threshold)).doubleValue()));
+		cq.orderBy(cb.desc(caseRoot.get(Case.REPORT_DATE)));
 
 		List<String> caseUuids = em.createQuery(cq).getResultList();
-		return caseUuids.size() == 1 ? caseUuids.get(0) : null;
+		return caseUuids.isEmpty() ? null : caseUuids.get(0);
 	}
 }

sormas-backend/src/main/java/de/symeda/sormas/backend/externalmessage/labmessage/AutomaticLabMessageProcessor.java

@@ -171,20 +171,31 @@ protected void handlePickOrCreateEntry(
 				result.setNewCase(true);
 				callback.done(result);
 			} else {
+				Disease disease = externalMessageDto.getDisease();
+				Integer automaticSampleAssignmentThreshold = diseaseConfigurationFacade.getAutomaticSampleAssignmentThreshold(disease);
+				if (automaticSampleAssignmentThreshold == null) {
+					logger.debug(
+						"[MESSAGE PROCESSING] No automatic sample assignment threshold configured for disease {}. Canceling processing.",
+						disease);
+					callback.cancel();
+					return;
+				}
+
 				Set<String> similarCaseUuids = similarCases.stream().map(CaseSelectionDto::getUuid).collect(Collectors.toSet());
-				String caseUuid = caseService.getCaseUuidForAutomaticSampleAssignment(similarCaseUuids, similarCases.get(0).getDisease());
+				String caseUuid = caseService.getCaseUuidForAutomaticSampleAssignment(similarCaseUuids, disease, automaticSampleAssignmentThreshold);
 
-				if (caseUuid != null) {
+				if (caseUuid == null) {
+					logger.debug(
+						"[MESSAGE PROCESSING] None of the similar cases {} is usable for automatic sample assignment. Continue with case creation.",
+						similarCaseUuids);
+					result.setNewCase(true);
+				} else {
 					CaseSelectionDto caseToAssignTo =
 						similarCases.stream().filter(c -> c.getUuid().equals(caseUuid)).findFirst().orElseThrow(IllegalStateException::new);
 					result.setCaze(caseToAssignTo);
-					callback.done(result);
-				} else {
-					logger.debug(
-						"[MESSAGE PROCESSING] None of the similar cases {} is usable for automatic sample assignment. Canceling processing.",
-						similarCaseUuids);
-					callback.cancel();
 				}
+
+				callback.done(result);
 			}
 		}
 

sormas-backend/src/test/java/de/symeda/sormas/backend/externalmessage/labmessage/AutomaticLabMessageProcessorTest.java

@@ -186,9 +186,13 @@ public void testProcessWithExistingPersonAndCase() throws ExecutionException, In
 		getCaseFacade().save(caze);
 
 		result = runFlow(externalMessage);
-		assertThat(result.getStatus(), is(CANCELED));
-		assertThat(externalMessage.getStatus(), is(ExternalMessageStatus.UNPROCESSED));
-		assertThat(getExternalMessageFacade().getByUuid(externalMessage.getUuid()).getStatus(), is(ExternalMessageStatus.UNPROCESSED));
+		assertThat(result.getStatus(), is(DONE));
+		assertThat(externalMessage.getStatus(), is(ExternalMessageStatus.PROCESSED));
+		assertThat(getExternalMessageFacade().getByUuid(externalMessage.getUuid()).getStatus(), is(ExternalMessageStatus.PROCESSED));
+		List<CaseDataDto> cases = getCaseFacade().getAllAfter(new Date(0));
+		assertThat(cases, hasSize(2));
+		CaseDataDto newCase = cases.stream().filter(c -> !DataHelper.isSame(c, caze)).findFirst().get();
+		assertThat(newCase.getPerson(), is(caze.getPerson()));
 
 		// set the case report after the threshold
 		caze.setReportDate(DateHelper.subtractDays(new Date(), 5));
@@ -201,17 +205,15 @@ public void testProcessWithExistingPersonAndCase() throws ExecutionException, In
 		List<PersonDto> persons = getPersonFacade().getAllAfter(new Date(0));
 		assertThat(persons, hasSize(1));
 		assertThat(persons.get(0).getUuid(), is(person.getUuid()));
-		List<CaseDataDto> cases = getCaseFacade().getByPersonUuids(persons.stream().map(PersonDto::getUuid).collect(Collectors.toList()));
-		assertThat(cases, hasSize(1));
-		assertThat(cases.get(0).getUuid(), is(caze.getUuid()));
-		List<SampleDto> samples = getSampleFacade().getByCaseUuids(cases.stream().map(CaseDataDto::getUuid).collect(Collectors.toList()));
-		assertThat(samples, hasSize(1));
-		List<PathogenTestDto> pathogenTests = getPathogenTestFacade().getAllBySample(samples.get(0).toReference());
-		assertThat(pathogenTests, hasSize(1));
+		cases = getCaseFacade().getByPersonUuids(persons.stream().map(PersonDto::getUuid).collect(Collectors.toList()));
+		assertThat(cases, hasSize(2));
+		// the sample should be added on the new case
+		List<SampleDto> samples = getSampleFacade().getByCaseUuids(Collections.singletonList(newCase.getUuid()));
+		assertThat(samples, hasSize(2));
 	}
 
 	@Test
-	public void testProcessWithExistingPersonAndCaseWithSample() throws ExecutionException, InterruptedException {
+	public void testProcessWithExistingPersonAndCaseWithBySampleDate() throws ExecutionException, InterruptedException {
 		ExternalMessageDto externalMessage = createExternalMessage(null);
 
 		PersonDto person =
@@ -220,6 +222,7 @@ public void testProcessWithExistingPersonAndCaseWithSample() throws ExecutionExc
 			});
 
 		CaseDataDto caze = creator.createCase(reportingUser.toReference(), person.toReference(), rdcf, c -> {
+			c.setReportDate(DateHelper.subtractDays(new Date(), 1));
 			c.setDisease(externalMessage.getDisease());
 		});
 
@@ -240,8 +243,13 @@ public void testProcessWithExistingPersonAndCaseWithSample() throws ExecutionExc
 		getSampleFacade().saveSample(sample);
 
 		result = runFlow(externalMessage);
-		assertThat(result.getStatus(), is(CANCELED));
-		assertThat(externalMessage.getStatus(), is(ExternalMessageStatus.UNPROCESSED));
+		assertThat(result.getStatus(), is(DONE));
+		assertThat(externalMessage.getStatus(), is(ExternalMessageStatus.PROCESSED));
+
+		List<PersonDto> persons = getPersonFacade().getAllAfter(new Date(0));
+		List<CaseDataDto> cases = getCaseFacade().getByPersonUuids(persons.stream().map(PersonDto::getUuid).collect(Collectors.toList()));
+		assertThat(cases, hasSize(2));
+		CaseDataDto newCase = cases.stream().filter(c -> !DataHelper.isSame(c, caze)).findFirst().get();
 
 		// set the sample date time after the threshold
 		sample.setSampleDateTime(DateHelper.subtractDays(new Date(), 5));
@@ -251,13 +259,12 @@ public void testProcessWithExistingPersonAndCaseWithSample() throws ExecutionExc
 		assertThat(result.getStatus(), is(DONE));
 		assertThat(externalMessage.getStatus(), is(ExternalMessageStatus.PROCESSED));
 
-		List<PersonDto> persons = getPersonFacade().getAllAfter(new Date(0));
+		persons = getPersonFacade().getAllAfter(new Date(0));
 		assertThat(persons, hasSize(1));
 		assertThat(persons.get(0).getUuid(), is(person.getUuid()));
-		List<CaseDataDto> cases = getCaseFacade().getByPersonUuids(persons.stream().map(PersonDto::getUuid).collect(Collectors.toList()));
-		assertThat(cases, hasSize(1));
-		assertThat(cases.get(0).getUuid(), is(caze.getUuid()));
-		List<SampleDto> samples = getSampleFacade().getByCaseUuids(cases.stream().map(CaseDataDto::getUuid).collect(Collectors.toList()));
+		cases = getCaseFacade().getByPersonUuids(persons.stream().map(PersonDto::getUuid).collect(Collectors.toList()));
+		assertThat(cases, hasSize(2));
+		List<SampleDto> samples = getSampleFacade().getByCaseUuids(Collections.singletonList(newCase.getUuid()));
 		assertThat(samples, hasSize(2));
 		SampleDto processedSample = samples.stream().filter(s -> !DataHelper.isSame(s, sample)).findFirst().get();
 		List<PathogenTestDto> pathogenTests = getPathogenTestFacade().getAllBySample(processedSample.toReference());