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Check if CMO label already exists in SMILE #83

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Nov 25, 2024
Merged

Check if CMO label already exists in SMILE #83

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93 changes: 89 additions & 4 deletions src/main/java/org/mskcc/smile/service/impl/LabelGenMessageHandlingServiceImpl.java
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Original file line number Diff line number Diff line change
Expand Up @@ -66,6 +66,9 @@ public class LabelGenMessageHandlingServiceImpl implements MessageHandlingServic
@Value("${request_reply.patient_samples_topic:}")
private String PATIENT_SAMPLES_REQUEST_TOPIC;

@Value("${request_reply.samples_by_cmo_label_topic}")
private String SAMPLES_BY_CMO_LABEL_REQREPLY_TOPIC;

@Autowired
private CmoLabelGeneratorService cmoLabelGeneratorService;

Expand Down Expand Up @@ -272,10 +275,25 @@ public void run() {
+ ", newly generated CMO label (using)="
+ newSampleCmoLabel);
} else {
LOG.info("Using existing CMO label for incoming sample: "
+ sampleManifest.getIgoId() + ", existing CMO label: "
+ sampleManifest.getCmoSampleName());
resolvedCmoSampleLabel = sampleManifest.getCmoSampleName();
// before settling on using the provided cmo label from the
// incoming sample check if that label already exists in smile
// for another sample
if (isCmoLabelAlreadyInUse(sampleManifest.getIgoId(),
sampleManifest.getCmoSampleName())) {
LOG.info("Incoming sample: " + sampleManifest.getIgoId()
+ " sample manifest contains an existing CMO label: "
+ sampleManifest.getCmoSampleName() + " that is "
+ "already in use by another sample in SMILE. To "
+ "prevent duplicate labels from getting persisted "
+ "into SMILE, the new label generated will be used "
+ "instead: " + newSampleCmoLabel);
resolvedCmoSampleLabel = newSampleCmoLabel;
} else {
LOG.info("Using existing CMO label for incoming sample: "
+ sampleManifest.getIgoId() + ", existing CMO label: "
+ sampleManifest.getCmoSampleName());
resolvedCmoSampleLabel = sampleManifest.getCmoSampleName();
}
}
}
sampleMap.put("cmoSampleName", resolvedCmoSampleLabel);
Expand Down Expand Up @@ -378,6 +396,51 @@ public void run() {
// necessarily affect the cmo label generated
String resolvedCmoSampleLabel = resolveAndUpdateCmoSampleLabel(
sample.getPrimaryId(), existingSamples, newCmoSampleLabel);

// if existing cmo label isn't blank then determine if the update is a meaningful
// update with respect to the sample metadata
if (!StringUtils.isBlank(sample.getCmoSampleName())) {
// if incoming updated sample has an existing cmo label then check
// if there are any meaningful changes to the metadata that
// affects the sample type abbreviation or nucleic acid abbreviation
Boolean hasMeaningfulUpdate =
cmoLabelGeneratorService.igoSampleRequiresLabelUpdate(
newCmoSampleLabel,
sample.getCmoSampleName());
if (hasMeaningfulUpdate) {
LOG.warn("Incoming updated sample has existing CMO label but "
+ "the label generator indicates that a change to the "
+ "metadata or updates to the label generation rules has "
+ "resulted in a new sample type abbreviation or nucleic "
+ "acid abbreviation: primary id="
+ sample.getPrimaryId()
+ ", incoming CMO sample label (not using)="
+ sample.getCmoSampleName()
+ ", newly generated CMO label (using)="
+ newCmoSampleLabel);
} else {
// before settling on using the provided cmo label from the
// incoming sample check if that label already exists in smile
// for another sample
if (isCmoLabelAlreadyInUse(sample.getPrimaryId(),
resolvedCmoSampleLabel)) {
LOG.info("Incoming updated sample: " + sample.getPrimaryId()
+ " sample metadata has a resolved CMO label: "
+ resolvedCmoSampleLabel + " that is "
+ "already in use by another sample in SMILE. To "
+ "prevent duplicate labels from getting persisted "
+ "into SMILE, the new label generated will be used "
+ "instead: " + newCmoSampleLabel);
resolvedCmoSampleLabel = newCmoSampleLabel;
} else {
LOG.info("Using existing CMO label for incoming sample: "
+ sample.getPrimaryId() + ", existing CMO label: "
+ sample.getCmoSampleName());
resolvedCmoSampleLabel = sample.getCmoSampleName();
}
}
}
// update the sample label for data being sent to smile server
sample.setCmoSampleName(resolvedCmoSampleLabel);
}
String updatedSampleJson = mapper.writeValueAsString(sample);
Expand Down Expand Up @@ -495,6 +558,28 @@ private List<SampleMetadata> getExistingPatientSamples(String cmoPatientId) thro
return new ArrayList<>(Arrays.asList(ptSamples));
}

private List<SampleMetadata> getSamplesByCmoLabel(String cmoLabel) throws Exception {
Message reply = messagingGateway.request(SAMPLES_BY_CMO_LABEL_REQREPLY_TOPIC,
cmoLabel);
SampleMetadata[] samplesByCmoLabel = mapper.readValue(
new String(reply.getData(), StandardCharsets.UTF_8),
SampleMetadata[].class);
return new ArrayList<>(Arrays.asList(samplesByCmoLabel));
}

private Boolean isCmoLabelAlreadyInUse(String primaryId, String cmoLabel) throws Exception {
List<SampleMetadata> samplesByCmoLabel = getSamplesByCmoLabel(cmoLabel);
for (SampleMetadata sm : samplesByCmoLabel) {
// if there are any samples returned that aren't the same primary id
// as the one provided then that indicates that the cmo label already exists
// in smile and is associated with a different sample
if (!sm.getPrimaryId().equals(primaryId)) {
return Boolean.TRUE;
}
}
return Boolean.FALSE;
}

private String getRequestIdFromRequestJson(String requestJson) throws JsonProcessingException {
Map<String, Object> requestJsonMap = mapper.readValue(requestJson, Map.class);
return requestJsonMap.get("requestId").toString();
Expand Down
1 change: 1 addition & 0 deletions src/main/resources/application.properties.EXAMPLE
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Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ smile.sample_update_topic=
# request-reply topics
request_reply.patient_samples_topic=
request_reply.cmo_label_generator_topic=
request_reply.samples_by_cmo_label_topic=

# threading
num.new_request_handler_threads=
Expand Down