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Resolve KM plot censored event bug and add caching #11027

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merged 2 commits into from
Sep 30, 2024
Merged

Resolve KM plot censored event bug and add caching #11027

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0a32002
Resolve censored event bug and add caching
kalletlak Sep 27, 2024
fef066a
Update cache resolver
kalletlak Sep 27, 2024
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15 changes: 6 additions & 9 deletions src/main/java/org/cbioportal/service/impl/ClinicalEventServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -150,12 +150,13 @@ public List<ClinicalData> getSurvivalData(List<String> studyIds,
).toList();

List<ClinicalEvent> patientCensoredEvents = filterClinicalEvents(patientStartEvents, survivalRequest.getCensoredEventRequestIdentifier());
Map<String, ClinicalEvent> patientCensoredEventsById = patientCensoredEvents.stream().collect(Collectors.toMap(ClinicalEventServiceImpl::getKey, Function.identity()));

return patientStartEvents.stream()
.flatMap(event -> {
ClinicalData clinicalDataMonths = buildClinicalSurvivalMonths(attributeIdPrefix, event, survivalRequest, patientEndEvents, patientCensoredEvents);
ClinicalData clinicalDataMonths = buildClinicalSurvivalMonths(attributeIdPrefix, event, survivalRequest, patientEndEventsById, patientCensoredEventsById);
if (clinicalDataMonths == null) return Stream.empty();
ClinicalData clinicalDataStatus = buildClinicalSurvivalStatus(attributeIdPrefix, event, patientEndEvents);
ClinicalData clinicalDataStatus = buildClinicalSurvivalStatus(attributeIdPrefix, event, patientEndEventsById);

return Stream.of(clinicalDataMonths, clinicalDataStatus);
}).toList();
Expand Down Expand Up @@ -200,22 +201,19 @@ private List<ClinicalEvent> filterClinicalEvents(List<ClinicalEvent> patientEven

// only fetch end timeline events for patients that have endClinicalEventsMeta and start timeline events
List<ClinicalEvent> queriedPatientEvents = new ArrayList<>();
if (CollectionUtils.isNotEmpty(clinicalEventsMeta) && CollectionUtils.isNotEmpty(filteredStudyIds)) {
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Is this line causing the issue?

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Yes

if (CollectionUtils.isNotEmpty(filteredStudyIds)) {
queriedPatientEvents = clinicalEventRepository.getTimelineEvents(filteredStudyIds, filteredPatientIds, clinicalEventsMeta);
}
return queriedPatientEvents;
}

private ClinicalData buildClinicalSurvivalMonths(String attributeIdPrefix, ClinicalEvent event, SurvivalRequest survivalRequest, List<ClinicalEvent> patientEndEvents, List<ClinicalEvent> patientCensoredEvents) {
private ClinicalData buildClinicalSurvivalMonths(String attributeIdPrefix, ClinicalEvent event, SurvivalRequest survivalRequest, Map<String, ClinicalEvent> patientEndEventsById, Map<String, ClinicalEvent> patientCensoredEventsById) {
final String SURVIVAL_MONTH_ATTRIBUTE = attributeIdPrefix + "_MONTHS";
ClinicalData clinicalDataMonths = new ClinicalData();
clinicalDataMonths.setStudyId(event.getStudyId());
clinicalDataMonths.setPatientId(event.getPatientId());
clinicalDataMonths.setAttrId(SURVIVAL_MONTH_ATTRIBUTE);

Map<String, ClinicalEvent> patientEndEventsById = patientEndEvents.stream().collect(Collectors.toMap(ClinicalEventServiceImpl::getKey, Function.identity()));
Map<String, ClinicalEvent> patientCensoredEventsById = patientCensoredEvents.stream().collect(Collectors.toMap(ClinicalEventServiceImpl::getKey, Function.identity()));

ToIntFunction<ClinicalEvent> startPositionIdentifier = getPositionIdentifier(survivalRequest.getStartEventRequestIdentifier().getPosition());
ToIntFunction<ClinicalEvent> endPositionIdentifier = survivalRequest.getEndEventRequestIdentifier() == null ? ClinicalEvent::getStopDate : getPositionIdentifier(survivalRequest.getEndEventRequestIdentifier().getPosition());
ToIntFunction<ClinicalEvent> censoredPositionIdentifier = survivalRequest.getCensoredEventRequestIdentifier() == null ? ClinicalEvent::getStopDate : getPositionIdentifier(survivalRequest.getCensoredEventRequestIdentifier().getPosition());
Expand All @@ -241,8 +239,7 @@ private ClinicalData buildClinicalSurvivalMonths(String attributeIdPrefix, Clini
return clinicalDataMonths;
}

private ClinicalData buildClinicalSurvivalStatus(String attributeIdPrefix, ClinicalEvent event, List<ClinicalEvent> patientEndEvents) {
Map<String, ClinicalEvent> patientEndEventsById = patientEndEvents.stream().collect(Collectors.toMap(ClinicalEventServiceImpl::getKey, Function.identity()));
private ClinicalData buildClinicalSurvivalStatus(String attributeIdPrefix, ClinicalEvent event, Map<String, ClinicalEvent> patientEndEventsById) {

ClinicalData clinicalDataStatus = new ClinicalData();
clinicalDataStatus.setStudyId(event.getStudyId());
Expand Down
23 changes: 13 additions & 10 deletions src/main/java/org/cbioportal/web/ClinicalEventController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -16,14 +16,10 @@
import org.cbioportal.service.exception.StudyNotFoundException;
import org.cbioportal.web.config.InternalApiTags;
import org.cbioportal.web.config.annotation.InternalApi;
import org.cbioportal.web.parameter.ClinicalEventAttributeRequest;
import org.cbioportal.web.parameter.Direction;
import org.cbioportal.web.parameter.HeaderKeyConstants;
import org.cbioportal.web.parameter.PagingConstants;
import org.cbioportal.web.parameter.PatientIdentifier;
import org.cbioportal.web.parameter.Projection;
import org.cbioportal.web.parameter.*;
import org.cbioportal.web.parameter.sort.ClinicalEventSortBy;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.http.HttpHeaders;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
Expand Down Expand Up @@ -144,6 +140,15 @@ public ResponseEntity<List<ClinicalEvent>> fetchClinicalEventsMeta(
@Parameter(hidden = true) // prevent reference to this attribute in the swagger-ui interface. This attribute is needed for the @PreAuthorize tag above.
@Valid @RequestAttribute(required = false, value = "interceptedClinicalEventAttributeRequest") ClinicalEventAttributeRequest interceptedClinicalEventAttributeRequest) {

return new ResponseEntity<>(cachedClinicalEventsMeta(interceptedClinicalEventAttributeRequest), HttpStatus.OK);

}

@Cacheable(
cacheResolver = "staticRepositoryCacheOneResolver",
condition = "@cacheEnabledConfig.getEnabled()"
)
public List<ClinicalEvent> cachedClinicalEventsMeta(ClinicalEventAttributeRequest interceptedClinicalEventAttributeRequest) {
List<String> studyIds = new ArrayList<>();
List<String> patientIds = new ArrayList<>();
for (PatientIdentifier patientIdentifier : interceptedClinicalEventAttributeRequest.getPatientIdentifiers()) {
Expand All @@ -160,9 +165,7 @@ public ResponseEntity<List<ClinicalEvent>> fetchClinicalEventsMeta(
return clinicalEvent;
})
.toList();

return new ResponseEntity<>(clinicalEventService.getClinicalEventsMeta(
studyIds, patientIds, clinicalEventsRequest), HttpStatus.OK);

return clinicalEventService.getClinicalEventsMeta(
studyIds, patientIds, clinicalEventsRequest);
}
}
22 changes: 15 additions & 7 deletions src/main/java/org/cbioportal/web/SurvivalController.java
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Original file line number Diff line number Diff line change
Expand Up @@ -14,6 +14,7 @@
import org.cbioportal.web.parameter.PatientIdentifier;
import org.cbioportal.web.parameter.SurvivalRequest;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.cache.annotation.Cacheable;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
Expand All @@ -36,7 +37,7 @@
@Tag(name = "Survival", description = " ")
public class SurvivalController {
private final ClinicalEventService clinicalEventService;

@Autowired
public SurvivalController(ClinicalEventService clinicalEventService) {
this.clinicalEventService = clinicalEventService;
Expand All @@ -59,18 +60,25 @@ public ResponseEntity<List<ClinicalData>> fetchSurvivalData(
// prevent reference to this attribute in the swagger-ui interface. this attribute is needed for the @PreAuthorize tag above.
@Valid @RequestAttribute(required = false, value = "interceptedSurvivalRequest") SurvivalRequest interceptedSurvivalRequest) {

return new ResponseEntity<>(cachedSurvivalData(interceptedSurvivalRequest),
HttpStatus.OK);
}

@Cacheable(
cacheResolver = "staticRepositoryCacheOneResolver",
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Wondering why we need to use staticRepositoryCacheOneResolver at here, I think for the case with lots of permutations like this (study_ids with sample_ids) we should use generalRepositoryCacheResolver

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Sure. will update

condition = "@cacheEnabledConfig.getEnabled()"
)
public List<ClinicalData> cachedSurvivalData(SurvivalRequest interceptedSurvivalRequest) {
List<String> studyIds = new ArrayList<>();
List<String> patientIds = new ArrayList<>();
for (PatientIdentifier patientIdentifier : interceptedSurvivalRequest.getPatientIdentifiers()) {
studyIds.add(patientIdentifier.getStudyId());
patientIds.add(patientIdentifier.getPatientId());
}

List<ClinicalData> result = clinicalEventService.getSurvivalData(studyIds,
patientIds,
interceptedSurvivalRequest.getAttributeIdPrefix(),
interceptedSurvivalRequest);

return new ResponseEntity<>(result, HttpStatus.OK);
return clinicalEventService.getSurvivalData(studyIds,
patientIds,
interceptedSurvivalRequest.getAttributeIdPrefix(),
interceptedSurvivalRequest);
}
}
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