Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

#13217 [Automatic message processing] Check sample assignment thresho… #13218

Merged
merged 1 commit into from
Dec 18, 2024
Merged

#13217 [Automatic message processing] Check sample assignment thresho… #13218

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions sormas-backend/src/main/java/de/symeda/sormas/backend/caze/CaseService.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
import java.util.function.Function;
import java.util.stream.Collectors;

import javax.annotation.Nullable;
import javax.ejb.EJB;
import javax.ejb.LocalBean;
import javax.ejb.Stateless;
Expand Down Expand Up @@ -2345,7 +2346,9 @@ protected String getDeleteReferenceField(DeletionReference deletionReference) {
return super.getDeleteReferenceField(deletionReference);
}

public String getCaseUuidForAutomaticSampleAssignment(Set<String> uuids, Disease disease, int threshold) {
public String getCaseUuidForAutomaticSampleAssignment(Set<String> uuids, Disease disease, @Nullable Date sampleDateTime, int threshold) {
Date dateToCompareTo = sampleDateTime != null ? sampleDateTime : new Date();

CriteriaBuilder cb = em.getCriteriaBuilder();
CriteriaQuery<String> cq = cb.createQuery(String.class);
Root<Case> caseRoot = cq.from(Case.class);
Expand All @@ -2366,7 +2369,7 @@ public String getCaseUuidForAutomaticSampleAssignment(Set<String> uuids, Disease
ExtendedPostgreSQL94Dialect.DATE,
Date.class,
CriteriaBuilderHelper.coalesce(cb, Date.class, earliestSampleSq, caseRoot.get(Case.REPORT_DATE))),
cb.function(ExtendedPostgreSQL94Dialect.DATE, Date.class, cb.literal(new Date()))),
cb.function(ExtendedPostgreSQL94Dialect.DATE, Date.class, cb.literal(dateToCompareTo))),
Long.valueOf(TimeUnit.DAYS.toSeconds(threshold)).doubleValue()));
cq.orderBy(cb.desc(caseRoot.get(Case.REPORT_DATE)));

Expand Down
13 changes: 12 additions & 1 deletion ...ava/de/symeda/sormas/backend/externalmessage/labmessage/AutomaticLabMessageProcessor.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,10 @@
package de.symeda.sormas.backend.externalmessage.labmessage;

import java.text.Collator;
import java.util.Comparator;
import java.util.Date;
import java.util.List;
import java.util.Objects;
import java.util.Set;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.CompletionStage;
Expand All @@ -43,6 +46,7 @@
import de.symeda.sormas.api.event.EventParticipantDto;
import de.symeda.sormas.api.event.SimilarEventParticipantDto;
import de.symeda.sormas.api.externalmessage.ExternalMessageDto;
import de.symeda.sormas.api.externalmessage.labmessage.SampleReportDto;
import de.symeda.sormas.api.externalmessage.processing.ExternalMessageMapper;
import de.symeda.sormas.api.externalmessage.processing.ExternalMessageProcessingFacade;
import de.symeda.sormas.api.externalmessage.processing.ExternalMessageProcessingResult;
Expand Down Expand Up @@ -183,7 +187,14 @@ protected void handlePickOrCreateEntry(
}

Set<String> similarCaseUuids = similarCases.stream().map(CaseSelectionDto::getUuid).collect(Collectors.toSet());
String caseUuid = caseService.getCaseUuidForAutomaticSampleAssignment(similarCaseUuids, disease, automaticSampleAssignmentThreshold);
Date sampleDate = externalMessageDto.getSampleReports()
.stream()
.map(SampleReportDto::getSampleDateTime)
.filter(Objects::nonNull)
.min(Comparator.comparing(Date::getTime))
.orElse(null);
String caseUuid =
caseService.getCaseUuidForAutomaticSampleAssignment(similarCaseUuids, disease, sampleDate, automaticSampleAssignmentThreshold);

if (caseUuid == null) {
logger.debug(
Expand Down
38 changes: 38 additions & 0 deletions ...de/symeda/sormas/backend/externalmessage/labmessage/AutomaticLabMessageProcessorTest.java
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
import org.junit.jupiter.api.Test;

import de.symeda.sormas.api.Disease;
import de.symeda.sormas.api.caze.CaseCriteria;
import de.symeda.sormas.api.caze.CaseDataDto;
import de.symeda.sormas.api.externalmessage.ExternalMessageDto;
import de.symeda.sormas.api.externalmessage.ExternalMessageStatus;
Expand All @@ -46,6 +47,7 @@
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.SampleCriteria;
import de.symeda.sormas.api.sample.SampleDto;
import de.symeda.sormas.api.sample.SampleMaterial;
import de.symeda.sormas.api.sample.SamplePurpose;
Expand Down Expand Up @@ -213,6 +215,42 @@ public void testProcessWithExistingPersonAndCase() throws ExecutionException, In
assertThat(samples, hasSize(2));
}

/**
* External message with sample date in the threshold period should generate a new sample to the existing case
* @throws ExecutionException
* @throws InterruptedException
*/
@Test
public void testThresholdAgainstSampleDate() throws ExecutionException, InterruptedException {
ExternalMessageDto externalMessage = createExternalMessage(e -> {
e.getSampleReports().get(0).setSampleDateTime(DateHelper.subtractDays(new Date(), 10));
});

PersonDto person =
creator.createPerson(externalMessage.getPersonFirstName(), externalMessage.getPersonLastName(), externalMessage.getPersonSex(), p -> {
p.setNationalHealthId(externalMessage.getPersonNationalHealthId());
});

CaseDataDto caze = creator.createCase(reportingUser.toReference(), person.toReference(), rdcf, c -> {
c.setDisease(externalMessage.getDisease());
c.setReportDate(DateHelper.subtractDays(new Date(), 15));
});
creator.createSample(caze.toReference(), reportingUser.toReference(), rdcf.facility, s -> {
s.setSampleDateTime(DateHelper.subtractDays(new Date(), 15));
});

// set the threshold
creator.updateDiseaseConfiguration(externalMessage.getDisease(), true, true, true, true, null, 10);
getBean(DiseaseConfigurationFacadeEjb.DiseaseConfigurationFacadeEjbLocal.class).loadData();

ProcessingResult<ExternalMessageProcessingResult> result = runFlow(externalMessage);
assertThat(result.getStatus(), is(DONE));
assertThat(externalMessage.getStatus(), is(ExternalMessageStatus.PROCESSED));

assertThat(getCaseFacade().count(new CaseCriteria().person(caze.getPerson())), is(1L));
assertThat(getSampleFacade().count(new SampleCriteria().caze(caze.toReference())), is(2L));
}

@Test
public void testProcessWithExistingPersonAndCaseWithBySampleDate() throws ExecutionException, InterruptedException {
ExternalMessageDto externalMessage = createExternalMessage(null);
Expand Down
Loading