Handle sample metadata updates with patient swap (#706)

Now handles scenario where sample metadata updates can include a patient swap
Added unit tests specific for this scenario
Confirmed that the REST service works as expected

Signed-off-by: Angelica Ochoa <[email protected]>

model/src/main/java/org/mskcc/smile/model/SmilePatient.java

@@ -30,6 +30,11 @@ public class SmilePatient implements Serializable {
 
     public SmilePatient() {}
 
+    public SmilePatient(String aliasValue, String aliasNamespace) {
+        this.patientAliases = new ArrayList<>();
+        patientAliases.add(new PatientAlias(aliasValue, aliasNamespace));
+    }
+
     public UUID getSmilePatientId() {
         return smilePatientId;
     }

persistence/src/main/java/org/mskcc/smile/persistence/neo4j/SmileSampleRepository.java

@@ -105,4 +105,10 @@ void updateSamplePatientRelationship(@Param("smileSampleId") UUID smileSampleId,
             + "OR sm.cmoSampleName = $inputId "
             + "RETURN s;")
     SmileSample findSampleByInputId(@Param("inputId") String inputId);
+
+    @Query("MATCH (s: Sample {smileSampleId: $smileSampleId}) "
+            + "MATCH (s)<-[r:HAS_SAMPLE]-(p: Patient {smilePatientId: $smilePatientId}) "
+            + "DELETE r")
+    void removeSamplePatientRelationship(@Param("smileSampleId") UUID smileSampleId,
+            @Param("smilePatientId") UUID smilePatientId);
 }

pom.xml

@@ -48,10 +48,10 @@
     <testcontainers.version>1.16.0</testcontainers.version>
     <!-- smile messaging and shared entities dependency versions -->
     <smile_messaging_java.group>com.github.mskcc</smile_messaging_java.group>
-    <smile_messaging_java.version>1.3.3.RELEASE</smile_messaging_java.version>
+    <smile_messaging_java.version>1.3.4.RELEASE</smile_messaging_java.version>
     <!-- smile commons centralized config properties -->
     <smile_commons.group>com.github.mskcc</smile_commons.group>
-    <smile_commons.version>1.3.3.RELEASE</smile_commons.version>
+    <smile_commons.version>1.3.4.RELEASE</smile_commons.version>
     <!-- smile expected schema version -->
     <smile.schema_version>v2.2</smile.schema_version>
   </properties>

service/src/main/java/org/mskcc/smile/service/SmileSampleService.java

@@ -10,7 +10,7 @@
 
 public interface SmileSampleService {
     SmileSample saveSmileSample(SmileSample smileSample) throws Exception;
-    SmileSample fetchAndLoadSampleDetails(SmileSample smileSample) throws Exception;
+    SmileSample fetchAndLoadPatientDetails(SmileSample smileSample) throws Exception;
     Boolean updateSampleMetadata(SampleMetadata sampleMetadata) throws Exception;
     List<SmileSample> getMatchedNormalsBySample(SmileSample smileSample)
             throws Exception;
@@ -19,7 +19,8 @@ List<SmileSample> getMatchedNormalsBySample(SmileSample smileSample)
     SmileSample getResearchSampleByRequestAndIgoId(String requestId, String igoId) throws Exception;
     List<SmileSample> getResearchSamplesByRequestId(String requestId) throws Exception;
     List<SampleMetadata> getResearchSampleMetadataHistoryByIgoId(String igoId) throws Exception;
-    Boolean sampleHasMetadataUpdates(SampleMetadata existingSampleMetadata, SampleMetadata sampleMetadata)
+    Boolean sampleHasMetadataUpdates(SampleMetadata existingSampleMetadata,
+            SampleMetadata sampleMetadata, Boolean isResearchSample)
             throws Exception;
     PublishedSmileSample getPublishedSmileSample(UUID smileSampleId) throws Exception;
     List<PublishedSmileSample> getPublishedSmileSamplesByCmoPatientId(String cmoPatientId)

service/src/main/java/org/mskcc/smile/service/impl/ClinicalMessageHandlingServiceImpl.java

@@ -126,7 +126,7 @@ public void run() {
                                     mapper.writeValueAsString(smileSample));
                         } else if (sampleService.sampleHasMetadataUpdates(
                                 existingSample.getLatestSampleMetadata(),
-                                smileSample.getLatestSampleMetadata())) {
+                                smileSample.getLatestSampleMetadata(), Boolean.FALSE)) {
                             LOG.info("Found updates for sample - persisting to database: "
                                     + smileSample.getPrimarySampleAlias());
                             existingSample.updateSampleMetadata(smileSample.getLatestSampleMetadata());
@@ -180,7 +180,7 @@ public void run() {
                                     mapper.writeValueAsString(smileSample));
                         } else if (sampleService.sampleHasMetadataUpdates(
                                 existingSample.getLatestSampleMetadata(),
-                                smileSample.getLatestSampleMetadata())) {
+                                smileSample.getLatestSampleMetadata(), Boolean.FALSE)) {
                             LOG.info("Found updates for sample - persisting to database: "
                                     + smileSample.getPrimarySampleAlias());
                             existingSample.updateSampleMetadata(smileSample.getLatestSampleMetadata());
@@ -244,6 +244,11 @@ public void onMessage(Message msg, Object message) {
                             DmpSampleMetadata.class);
                     String cmoPatientId = crdbMappingService.getCmoPatientIdbyDmpId(
                             dmpSample.getDmpPatientId());
+                    if (cmoPatientId == null) {
+                        LOG.error("Could not resolve cmoPatientId from dmpId: "
+                                + dmpSample.getDmpPatientId());
+                        return;
+                    }
                     SmileSample sample = SampleDataFactory.buildNewClinicalSampleFromMetadata(
                             cmoPatientId, dmpSample);
                     clinicalMessageHandlingService.newClinicalSampleHandler(sample);
@@ -268,6 +273,11 @@ public void onMessage(Message msg, Object message) {
                             DmpSampleMetadata.class);
                     String cmoPatientId = crdbMappingService.getCmoPatientIdbyDmpId(
                             dmpSample.getDmpPatientId());
+                    if (cmoPatientId == null) {
+                        LOG.error("Could not resolve cmoPatientId from dmpId: "
+                                + dmpSample.getDmpPatientId());
+                        return;
+                    }
                     SmileSample sample = SampleDataFactory.buildNewClinicalSampleFromMetadata(
                             cmoPatientId, dmpSample);
                     clinicalMessageHandlingService.clinicalSampleUpdateHandler(sample);

service/src/main/java/org/mskcc/smile/service/impl/RequestServiceImpl.java

@@ -206,27 +206,15 @@ private Boolean timestampWithin24Hours(Date referenceTimestamp, Date newTimestam
 
     @Override
     public Boolean requestHasUpdates(SmileRequest existingRequest, SmileRequest request) throws Exception {
-        try {
-            jsonComparator.isConsistent(mapper.writeValueAsString(existingRequest),
-                mapper.writeValueAsString(request));
-        } catch (AssertionError e) {
-            LOG.warn("Found discrepancies between JSONs:\n" + e.getLocalizedMessage());
-            return Boolean.TRUE;
-        }
-        return Boolean.FALSE;
+        return !(jsonComparator.isConsistent(mapper.writeValueAsString(existingRequest),
+                mapper.writeValueAsString(request)));
     }
 
     @Override
     public Boolean requestHasMetadataUpdates(RequestMetadata existingRequestMetadata,
             RequestMetadata requestMetadata) throws Exception {
-        try {
-            jsonComparator.isConsistent(existingRequestMetadata.getRequestMetadataJson(),
-                    requestMetadata.getRequestMetadataJson());
-        } catch (AssertionError e) {
-            LOG.warn("Found discrepancies between JSONs:\n" + e.getLocalizedMessage());
-            return Boolean.TRUE;
-        }
-        return Boolean.FALSE;
+        return !(jsonComparator.isConsistent(existingRequestMetadata.getRequestMetadataJson(),
+                requestMetadata.getRequestMetadataJson()));
     }
 
     @Override
@@ -240,14 +228,10 @@ public List<SmileSample> getRequestSamplesWithUpdates(SmileRequest request) thro
             if (existingSample == null) {
                 continue;
             }
-            // compare sample metadata from current request and the saved request
-            String latestMetadata = mapper.writeValueAsString(existingSample.getLatestSampleMetadata());
-            String currentMetadata = mapper.writeValueAsString(sample.getLatestSampleMetadata());
-
-            try {
-                jsonComparator.isConsistent(latestMetadata, currentMetadata);
-            } catch (AssertionError e) {
-                LOG.warn("Found discrepancies between JSONs:\n" + e.getLocalizedMessage());
+            Boolean sampleHasUpdates = 
+                    sampleService.sampleHasMetadataUpdates(existingSample.getLatestSampleMetadata(),
+                    sample.getLatestSampleMetadata(), Boolean.TRUE);
+            if (sampleHasUpdates) {
                 existingSample.updateSampleMetadata(sample.getLatestSampleMetadata());
                 updatedSamples.add(existingSample);
             }

service/src/main/java/org/mskcc/smile/service/impl/ResearchMessageHandlingServiceImpl.java

@@ -53,6 +53,9 @@ public class ResearchMessageHandlingServiceImpl implements ResearchMessageHandli
     @Value("${smile.cmo_sample_update_topic}")
     private String CMO_SAMPLE_UPDATE_TOPIC;
 
+    @Value("${request_reply.cmo_label_generator_topic}")
+    private String CMO_LABEL_GENERATOR_REQREPLY_TOPIC;
+
     @Value("${num.new_request_handler_threads}")
     private int NUM_NEW_REQUEST_HANDLERS;
 
@@ -123,10 +126,10 @@ public void run() {
                             requestService.saveRequest(request);
                         } else {
                             // request-service and sample-service methods will check for updates and persist
-                            // them if applicable
+                            // them if applicable (including patient swapping)
                             requestService.updateRequestMetadata(request.getLatestRequestMetadata());
                             for (SmileSample sample : request.getSmileSampleList()) {
-                                sampleService.updateSampleMetadata(sample.getLatestSampleMetadata());
+                                sampleService.saveSmileSample(sample);
                             }
                         }
                         // publish updated/saved request to consistency checker or promoted request topic