Bug fix for CORRECT_CMO_PATIENT_ID workflow (#1017)

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

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

@@ -4,6 +4,6 @@
 
 public interface CrdbMappingService {
     String getCmoPatientIdbyDmpId(String dmpId);
-    String getCmoPatientIdByInputId(String inputId);
+    String getCmoPatientIdByInputId(String inputId) throws Exception;
     CrdbMappingModel getCrdbMappingModelByInputId(String inputId) throws Exception;
 }

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

@@ -1,6 +1,5 @@
 package org.mskcc.smile.service.impl;
 
-import com.fasterxml.jackson.core.JsonProcessingException;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import io.nats.client.Message;
 import java.nio.charset.StandardCharsets;
@@ -106,6 +105,8 @@ public void run() {
                         String oldCmoPtId = idCorrectionMap.get("oldId");
                         String newCmoPtId = idCorrectionMap.get("newId");
 
+                        // grab samples by old cmo patient id and new cmo patient id that
+                        // we are correcting or swapping to
                         List<SmileSample> samplesByOldCmoPatient =
                                 sampleService.getSamplesByCmoPatientId(oldCmoPtId);
                         List<SmileSample> samplesByNewCmoPatient =
@@ -192,26 +193,25 @@ private void setupCorrectCmoPatientIdHandler(Gateway gateway,
             public void onMessage(Message msg, Object message) {
                 LOG.info("Received message on topic: " + CORRECT_CMOPTID_TOPIC);
                 Map<String, String> incomingDataMap = new HashMap<>();
+                String oldCmoPatientId = null;
+                String newCmoPatientId = null;
                 try {
-                    // do not log contents of incoming message
                     String incomingDataString = mapper.readValue(
                             new String(msg.getData(), StandardCharsets.UTF_8),
                             String.class);
                     incomingDataMap = mapper.readValue(incomingDataString, Map.class);
-                } catch (JsonProcessingException e) {
-                    LOG.error("Error processing the incoming data map. "
-                            + "Refer to NATS logs for more details.");
+                    oldCmoPatientId = crdbMappingService.getCmoPatientIdByInputId(
+                                incomingDataMap.get("oldId"));
+                    newCmoPatientId = crdbMappingService.getCmoPatientIdByInputId(
+                                incomingDataMap.get("newId"));
+                } catch (Exception e) {
+                    LOG.error("Error parsing the incoming data map: ", e);
                 }
                 if (incomingDataMap.isEmpty()) {
                     LOG.error("Was not able to deserialize incoming message as instance of Map.class - "
                             + "please confirm manually that the expected message contents were published");
                 } else {
-                    String oldCmoPatientId = crdbMappingService.getCmoPatientIdByInputId(
-                            incomingDataMap.get("oldId"));
-                    String newCmoPatientId = crdbMappingService.getCmoPatientIdByInputId(
-                            incomingDataMap.get("newId"));
                     Boolean crdbMappingStatus = Boolean.TRUE;
-
                     // verify that old and new ids resolve to a valid cmo patient id in crdb service
                     if (oldCmoPatientId == null || oldCmoPatientId.isEmpty()) {
                         StringBuilder logMessage = new StringBuilder();
@@ -262,7 +262,6 @@ public void onMessage(Message msg, Object message) {
         });
     }
 
-
     @Override
     public void shutdown() throws Exception {
         if (!initialized) {

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

@@ -48,7 +48,7 @@ public Object call() {
     }
 
     @Override
-    public String getCmoPatientIdByInputId(String inputId) {
+    public String getCmoPatientIdByInputId(String inputId) throws Exception {
         Callable<Object> task = new Callable<Object>() {
             @Override
             public Object call() {
@@ -57,7 +57,9 @@ public Object call() {
         };
         Object result = runQueryWithForcedTimeout(task);
         if (result != null) {
-            return result.toString();
+            ArrayList<Object> crdbValues = mapper.convertValue(result, ArrayList.class);
+            CrdbMappingModel r = new CrdbMappingModel(crdbValues);
+            return r.getCmoId().replace("\"", "");
         }
         return null;
     }

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

@@ -81,14 +81,29 @@ public SmileSample saveSmileSample(SmileSample
             if (!existingSample.getSampleClass().equals(sampleMetadata.getTumorOrNormal())) {
                 existingSample.setSampleClass(sampleMetadata.getTumorOrNormal());
             }
-            // determine where a patient swap is required also
+
+            // determine whether a patient swap is required also
             if (!sample.getPatient().getSmilePatientId().equals(
                     existingSample.getPatient().getSmilePatientId())) {
                 LOG.info("Updating sample-to-patient relationship and removing connection to patient: "
                         + existingSample.getPatient().getSmilePatientId());
                 sampleRepository.removeSamplePatientRelationship(existingSample.getSmileSampleId(),
                         existingSample.getPatient().getSmilePatientId());
-                existingSample.setPatient(sample.getPatient());
+                // merge aliases from existing patient to the patient we are swapping to
+                SmilePatient existingPatient = existingSample.getPatient();
+                SmilePatient patientToSwapTo = sample.getPatient();
+                Boolean updatedPatientAliases = Boolean.FALSE;
+                for (PatientAlias pa : existingPatient.getPatientAliases()) {
+                    if (!patientToSwapTo.hasPatientAlias(pa)) {
+                        patientToSwapTo.addPatientAlias(pa);
+                        updatedPatientAliases = Boolean.TRUE;
+                    }
+                }
+                // save updates to patient we are swapping to if applicable
+                if (updatedPatientAliases) {
+                    patientService.savePatientMetadata(patientToSwapTo);
+                }
+                existingSample.setPatient(patientToSwapTo);
             }
             sampleRepository.save(existingSample);
             toReturn = existingSample;
@@ -254,7 +269,7 @@ public Boolean updateSampleMetadata(SampleMetadata sampleMetadata, Boolean fromL
             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());
@@ -361,7 +376,8 @@ public List<PublishedSmileSample> getPublishedSmileSamplesByCmoPatientId(
     @Override
     public List<SmileSample> getSamplesByCmoPatientId(String cmoPatientId) throws Exception {
         List<SmileSample> samples = new ArrayList<>();
-        for (SmileSample sample: sampleRepository.findAllSamplesByCmoPatientId(cmoPatientId)) {
+        List<SmileSample> samplesFound = sampleRepository.findAllSamplesByCmoPatientId(cmoPatientId);
+        for (SmileSample sample: samplesFound) {
             samples.add(getDetailedSmileSample(sample));
         }
         return samples;