test dmpId (#732)

* test dmpId Signed-off-by: Divya Madala <[email protected]> * working changes Signed-off-by: Divya Madala <[email protected]> * matcher Signed-off-by: Divya Madala <[email protected]>
mskcc · Jul 8, 2022 · 1fe506f · 1fe506f
1 parent 881b210
commit 1fe506f
Showing 1 changed file with 10 additions and 0 deletions.
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java
@@ -6,6 +6,8 @@
 import java.util.ArrayList;
 import java.util.List;
 import java.util.UUID;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 import org.mskcc.smile.commons.JsonComparator;
@@ -28,6 +30,7 @@
 
 @Component
 public class SampleServiceImpl implements SmileSampleService {
+    private static final Pattern DMP_PATIENT_ID = Pattern.compile("P-\\d*");
     @Autowired
     private JsonComparator jsonComparator;
 
@@ -139,6 +142,13 @@ public SmileSample fetchAndLoadPatientDetails(SmileSample sample) throws Excepti
         // 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