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Merged
ao508 merged 4 commits into from
May 22, 2026
Merged

Npe handling sample updates #1870

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aa00187
Move operation to set revisable=true out of transactional operations
ao508 May 20, 2026
3de5570
Set log-level to default for req-rep handlers
ao508 May 20, 2026
3dce69e
Handle NPE when existing sample class is null or empty
ao508 May 21, 2026
e85609e
Checkstyle fix
ao508 May 21, 2026
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7 changes: 7 additions & 0 deletions model/src/main/java/org/mskcc/smile/model/SmileSample.java
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Original file line number Diff line number Diff line change
Expand Up @@ -187,6 +187,7 @@ public void applyIgoLimsUpdates(SampleMetadata sampleMetadata) throws ParseExcep
SampleMetadata latestSampleMetadata = getLatestSampleMetadata();

sampleMetadata.setId(null);
this.sampleClass = latestSampleMetadata.getTumorOrNormal();
sampleMetadata.setCmoPatientId(latestSampleMetadata.getCmoPatientId());
sampleMetadata.setInvestigatorSampleId(latestSampleMetadata.getInvestigatorSampleId());
sampleMetadata.setSampleName(latestSampleMetadata.getSampleName());
Expand All @@ -205,8 +206,14 @@ public void applyIgoLimsUpdates(SampleMetadata sampleMetadata) throws ParseExcep
addSampleMetadata(sampleMetadata);
}

/**
* Updates sample instance with given metadata.
* @param sampleMetadata
* @throws ParseException
*/
public void updateSampleMetadata(SampleMetadata sampleMetadata) throws ParseException {
sampleMetadata.setId(null);
this.sampleClass = sampleMetadata.getTumorOrNormal();
addSampleMetadata(sampleMetadata);
}

Expand Down
1 change: 1 addition & 0 deletions service/src/main/java/org/mskcc/smile/service/SmileSampleService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,4 +42,5 @@ List<SmileSample> getSamplesByCategoryAndCmoPatientId(String cmoPatientId,
List<String> getSamplePrimaryIdsBySmileTempoIds(List<UUID> smileTempoIds) throws Exception;
String getSamplePrimaryIdBySampleInputId(String inputId) throws Exception;
Map<String, Object> getMatchedAndUnmatchedInputSampleIds(List<String> inputIds) throws Exception;
void setSampleRevisableTrue(UUID smileSampleId);
}
4 changes: 4 additions & 0 deletions service/src/main/java/org/mskcc/smile/service/impl/ClinicalMessageHandlingServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -122,6 +122,7 @@ public void run() {
+ smileSample.getPrimarySampleAlias());

sampleService.saveSmileSample(smileSample);
sampleService.setSampleRevisableTrue(smileSample.getSmileSampleId());
LOG.info("Publishing metadata history for new sample: "
+ smileSample.getPrimarySampleAlias());
messagingGateway.publish(CONS_DMP_NEW_SAMPLE_TOPIC,
Expand All @@ -133,6 +134,7 @@ public void run() {
+ smileSample.getPrimarySampleAlias());
existingSample.updateSampleMetadata(smileSample.getLatestSampleMetadata());
sampleService.saveSmileSample(existingSample);
sampleService.setSampleRevisableTrue(existingSample.getSmileSampleId());
messagingGateway.publish(CONS_DMP_SAMPLE_UPDATE_TOPIC,
mapper.writeValueAsString(smileSample));
} else {
Expand Down Expand Up @@ -176,6 +178,7 @@ public void run() {
+ smileSample.getPrimarySampleAlias());

sampleService.saveSmileSample(smileSample);
sampleService.setSampleRevisableTrue(smileSample.getSmileSampleId());
LOG.info("Publishing metadata history for new sample: "
+ smileSample.getPrimarySampleAlias());
messagingGateway.publish(CONS_DMP_NEW_SAMPLE_TOPIC,
Expand All @@ -187,6 +190,7 @@ public void run() {
+ smileSample.getPrimarySampleAlias());
existingSample.updateSampleMetadata(smileSample.getLatestSampleMetadata());
sampleService.saveSmileSample(existingSample);
sampleService.setSampleRevisableTrue(existingSample.getSmileSampleId());
messagingGateway.publish(CONS_DMP_SAMPLE_UPDATE_TOPIC,
mapper.writeValueAsString(smileSample));
} else {
Expand Down
1 change: 1 addition & 0 deletions service/src/main/java/org/mskcc/smile/service/impl/CorrectCmoPatientHandlingServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -164,6 +164,7 @@ public void run() {
// the cmo patient id we are swapping to
sample.updateSampleMetadata(updatedMetadata);
sampleService.saveSmileSample(sample);
sampleService.setSampleRevisableTrue(sample.getSmileSampleId());
}

// sample service is handling patient swapping now so we can simply rely on deleting
Expand Down
8 changes: 4 additions & 4 deletions service/src/main/java/org/mskcc/smile/service/impl/RequestReplyHandlingServiceImpl.java
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Expand Up @@ -331,7 +331,7 @@ private void setupPatientSamplesHandler(Gateway gateway,
gateway.replySub(PATIENT_SAMPLES_REQREPLY_TOPIC, new MessageConsumer() {
@Override
public void onMessage(Message msg, Object message) {
LOG.info("Received message on topic: " + PATIENT_SAMPLES_REQREPLY_TOPIC);
LOG.debug("Received message on topic: " + PATIENT_SAMPLES_REQREPLY_TOPIC);
try {
if (StringUtils.isBlank(new String(msg.getData()))) {
LOG.error("Expected a patient ID but message received is empty: " + msg
Expand All @@ -353,7 +353,7 @@ private void setupSamplesByCmoLabelHandler(Gateway gateway,
gateway.replySub(SAMPLES_BY_CMO_LABEL_REQREPLY_TOPIC, new MessageConsumer() {
@Override
public void onMessage(Message msg, Object message) {
LOG.info("Received message on topic: " + SAMPLES_BY_CMO_LABEL_REQREPLY_TOPIC);
LOG.debug("Received message on topic: " + SAMPLES_BY_CMO_LABEL_REQREPLY_TOPIC);
try {
if (StringUtils.isBlank(new String(msg.getData()))) {
LOG.error("Expected a CMO label but message received is empty: " + msg
Expand All @@ -375,7 +375,7 @@ private void setupSamplesByAltIdHandler(Gateway gateway,
gateway.replySub(SAMPLES_BY_ALT_ID_REQREPLY_TOPIC, new MessageConsumer() {
@Override
public void onMessage(Message msg, Object message) {
LOG.info("Received message on topic: " + SAMPLES_BY_ALT_ID_REQREPLY_TOPIC);
LOG.debug("Received message on topic: " + SAMPLES_BY_ALT_ID_REQREPLY_TOPIC);
try {
if (StringUtils.isBlank(new String(msg.getData()))) {
LOG.error("Expected an alt ID but message received is empty: " + msg
Expand All @@ -397,7 +397,7 @@ private void setupPatientIdMappingHandler(Gateway gateway,
gateway.replySub(PATIENT_MAPPING_REQREPLY_TOPIC, new MessageConsumer() {
@Override
public void onMessage(Message msg, Object message) {
LOG.info("Received message on topic: " + PATIENT_MAPPING_REQREPLY_TOPIC);
LOG.debug("Received message on topic: " + PATIENT_MAPPING_REQREPLY_TOPIC);
try {
requestReplyHandlingServiceImpl.patientIdMappingHandler(
new String(msg.getData()), msg.getReplyTo());
Expand Down
4 changes: 3 additions & 1 deletion service/src/main/java/org/mskcc/smile/service/impl/RequestServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,9 @@ public Boolean saveRequest(SmileRequest request) throws Exception {
for (SmileSample s: request.getSmileSampleList()) {
// considering adding the patientService.savePatient() stuff here
// and remove from the sample service.
updatedSamples.add(sampleService.saveSmileSample(s));
sampleService.saveSmileSample(s);
sampleService.setSampleRevisableTrue(s.getSmileSampleId());
updatedSamples.add(s);
}
request.setSmileSampleList(updatedSamples);
}
Expand Down
10 changes: 6 additions & 4 deletions service/src/main/java/org/mskcc/smile/service/impl/ResearchMessageHandlingServiceImpl.java
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Expand Up @@ -241,11 +241,12 @@ public void run() {
100, TimeUnit.MILLISECONDS);
if (sampleMetadataEntry != null) {
// Boolean arg in updateSampleMetadata refers to fromLims
SmileSample existingSample = sampleService.getResearchSampleByRequestAndIgoId(
sampleMetadataEntry.getValue().getIgoRequestId(),
sampleMetadataEntry.getValue().getPrimaryId());
Boolean fromLims = sampleMetadataEntry.getKey();
if (sampleService.updateSampleMetadata(sampleMetadataEntry.getValue(),
sampleMetadataEntry.getKey())) {
SmileSample existingSample = sampleService.getResearchSampleByRequestAndIgoId(
sampleMetadataEntry.getValue().getIgoRequestId(),
sampleMetadataEntry.getValue().getPrimaryId());
fromLims)) {
// temp patch to avoid deep-nested circular writing of
// sample -> tempo - > sample etc.
// tempo isn't needed when publishing sample metadata history
Expand All @@ -265,6 +266,7 @@ public void run() {
Arrays.asList(sampleMetadataEntry.getValue().getPrimaryId()));
}
}
sampleService.setSampleRevisableTrue(existingSample.getSmileSampleId());
}
if (interrupted && researchSampleUpdateQueue.isEmpty()) {
break;
Expand Down
40 changes: 19 additions & 21 deletions service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,8 @@ public SmileSample saveSmileSample(SmileSample

// If there is a TumorOrNormal update in SampleMetadata level,
// then sampleClass should also be updated in the SmileSample level
if (!existingSample.getSampleClass().equals(sampleMetadata.getTumorOrNormal())) {
if (StringUtils.isBlank(existingSample.getSampleClass())
|| !existingSample.getSampleClass().equals(sampleMetadata.getTumorOrNormal())) {
existingSample.setSampleClass(sampleMetadata.getTumorOrNormal());
}

Expand Down Expand Up @@ -128,8 +129,6 @@ public SmileSample saveSmileSample(SmileSample
sampleRepository.save(existingSample);
toReturn = existingSample;
}
// update revisable to true for sample
sampleRepository.updateRevisableBySampleId(toReturn.getSmileSampleId(), Boolean.TRUE);
return toReturn;
}

Expand Down Expand Up @@ -292,14 +291,6 @@ public Boolean updateSampleMetadata(SampleMetadata sampleMetadata, Boolean fromL
saveSmileSample(existingSample);
return Boolean.TRUE;
}
// if sample revisable is false then return true so that message handler
// publishes message downstream (allows dashboard to make changes to db directly
// without having to wait or poll for updates)
if (!existingSample.getRevisable()) {
sampleRepository.updateRevisableBySampleId(existingSample.getSmileSampleId(), Boolean.TRUE);
return Boolean.TRUE;
}

// no updates to persist to sample, log and return false
LOG.info("There are no updates to persist for sample: "
+ sampleMetadata.getPrimaryId());
Expand Down Expand Up @@ -359,32 +350,34 @@ public List<SampleMetadata> getResearchSampleMetadataHistoryByIgoId(String igoId
}

@Override
public Boolean sampleHasMetadataUpdates(SampleMetadata existingSampleMetadata,
SampleMetadata sampleMetadata, Boolean isResearchSample, Boolean fromLims) throws Exception {
String existingMetadata = mapper.writeValueAsString(existingSampleMetadata);
String currentMetadata = mapper.writeValueAsString(sampleMetadata);
public Boolean sampleHasMetadataUpdates(SampleMetadata existingMetadata,
SampleMetadata newMetadata, Boolean isResearchSample, Boolean fromLims) throws Exception {
String existingMetadataStr = mapper.writeValueAsString(existingMetadata);
String newMetadataStr = mapper.writeValueAsString(newMetadata);
// if sample is from LIMS, look for updates by igo properties
if (fromLims && !jsonComparator.isConsistentByIgoProperties(currentMetadata, existingMetadata)) {
if (fromLims && !jsonComparator.isConsistentByIgoProperties(newMetadataStr, existingMetadataStr)) {
return Boolean.TRUE;
}
// if sample is not from LIMS, look for updates by all properties
if (!fromLims && !jsonComparator.isConsistent(currentMetadata, existingMetadata)) {
if (!fromLims && !jsonComparator.isConsistent(newMetadataStr, existingMetadataStr)) {
return Boolean.TRUE;
}
// if there is a change to the cmo sample label..
if (isResearchSample) {
String currentLabel = existingSampleMetadata.getCmoSampleName();
String newLabel = sampleMetadata.getCmoSampleName();
String currentLabel = existingMetadata.getCmoSampleName();
String newLabel = newMetadata.getCmoSampleName();
if ((!StringUtils.isBlank(currentLabel) && !currentLabel.equals(newLabel))
|| (StringUtils.isBlank(currentLabel) && !StringUtils.isBlank(newLabel))) {
return Boolean.TRUE;
}
}

// if there needs to be a patient swap..
if (!existingSampleMetadata.getCmoPatientId()
.equals(sampleMetadata.getCmoPatientId())) {
if (StringUtils.isBlank(existingMetadata.getCmoPatientId())
|| !existingMetadata.getCmoPatientId().equals(newMetadata.getCmoPatientId())) {
return Boolean.TRUE;
}

return Boolean.FALSE;
}

Expand Down Expand Up @@ -556,4 +549,9 @@ public String getSamplePrimaryIdBySampleInputId(String inputId) throws Exception
public Map<String, Object> getMatchedAndUnmatchedInputSampleIds(List<String> inputIds) throws Exception {
return sampleRepository.findMatchedAndUnmatchedInputSampleIds(inputIds);
}

@Override
public void setSampleRevisableTrue(UUID smileSampleId) {
sampleRepository.updateRevisableBySampleId(smileSampleId, Boolean.TRUE);
}
}