Bug fix for duplicating new patient nodes (#1081)

Patient nodes were getting duplicated under specific circumstances:
- patient does not already exist in the database
- more than one sample in a new incoming request share the same patient

These changes and rearrangement of some of the logic handle how the patient
is resolved per incoming sample should now work for both existing and new patients.

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

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

@@ -48,7 +48,6 @@ public class SampleServiceImpl implements SmileSampleService {
     @Autowired
     private CrdbMappingService crdbMappingService;
 
-
     private static final Log LOG = LogFactory.getLog(SampleServiceImpl.class);
     private final ObjectMapper mapper = new ObjectMapper();
 
@@ -166,13 +165,15 @@ public SmileSample fetchAndLoadPatientDetails(SmileSample sample) throws Excepti
 
         // handle the scenario where a patient node does not already exist in the database
         // to prevent any null pointer exceptions (a situation that had arose in some test dmp sample cases)
-        if (patientService.getPatientByCmoPatientId(
-               sample.getPatient().getCmoPatientId().getValue()) == null) {
+        if (patientService.getPatientByCmoPatientId(patient.getCmoPatientId().getValue()) == null) {
             patientService.savePatientMetadata(patient);
             sample.setPatient(patient);
         }
 
         // get patient by cmo id from latest sample metadata
+        // note: the patient according to the cmo id in the sample's latest metadata may
+        // not match the patient that is linked to an existing sample in the event
+        // that a patient swap is needed and is the reason for the incoming sample update
         SmilePatient patientByLatestCmoId = patientService.getPatientByCmoPatientId(
                 sampleMetadata.getCmoPatientId());
 
@@ -183,28 +184,8 @@ public SmileSample fetchAndLoadPatientDetails(SmileSample sample) throws Excepti
                     + "- confirm whether data construction and parsing is being handled correctly");
         }
 
-        // scenario that requires a patient swap and updating the sample-to-patient relationship
-        // in the database and removing the former sample-to-patient relationship
-        if (patientByLatestCmoId == null) {
-            SmilePatient newPatient = new SmilePatient(sampleMetadata.getCmoPatientId(), "cmoId");
-            //if this sample is a clinical sample, we would also need to add dmpId
-            if (sample.getSampleCategory().equals("clinical")) {
-                Matcher matcher = DMP_PATIENT_ID.matcher(sampleMetadata.getPrimaryId());
-                if (matcher.find()) {
-                    newPatient.addPatientAlias(new PatientAlias(matcher.group(), "dmpId"));
-                }
-            }
-            patientService.savePatientMetadata(newPatient);
-            sample.setPatient(newPatient);
-            // remove sample-to-patient relationship from former patient node
-            sampleRepository.removeSamplePatientRelationship(sample.getSmileSampleId(),
-                    patient.getSmilePatientId());
-            return sample;
-        }
-
-        // scenario where we are checking for an update to the existing patient, which is the same
-        // that already existing and is linked to the sample in the database but may contain updates
-        // (i.e., a new patient alias)
+        // scenario where we are checking for an update to the existing patient and is linked to the
+        // sample in the database but may contain updates (i.e., a new patient alias)
         if (patient.getCmoPatientId().getValue().equals(sampleMetadata.getCmoPatientId())) {
             // go through the new patient aliases and indicator for whether a
             // new patient alias was added to the existing patient
@@ -223,6 +204,26 @@ public SmileSample fetchAndLoadPatientDetails(SmileSample sample) throws Excepti
             return sample;
         }
 
+        // scenario that requires a patient swap and updating the sample-to-patient relationship
+        // in the database and removing the former sample-to-patient relationship
+        if (patientByLatestCmoId == null) {
+            SmilePatient newPatient = new SmilePatient(sampleMetadata.getCmoPatientId(), "cmoId");
+            //if this sample is a clinical sample, we would also need to add dmpId
+            if (sample.getSampleCategory().equals("clinical")
+                    && !sample.getPatient().hasPatientAlias("dmpId")) {
+                Matcher matcher = DMP_PATIENT_ID.matcher(sampleMetadata.getPrimaryId());
+                if (matcher.find()) {
+                    newPatient.addPatientAlias(new PatientAlias(matcher.group(), "dmpId"));
+                }
+            }
+            patientService.savePatientMetadata(newPatient);
+            sample.setPatient(newPatient);
+            // remove sample-to-patient relationship from former patient node
+            sampleRepository.removeSamplePatientRelationship(sample.getSmileSampleId(),
+                    patient.getSmilePatientId());
+            return sample;
+        }
+
         // scenario where the patient that the sample-to-patient relationship points to in the database
         // does not match the cmo patient id referenced in the latest sample metadata updates
         // and the former sample-to-patient relationship needs to be removed