From e39a5357e49cae2b0e6a4addd41275e6bd2c616c Mon Sep 17 00:00:00 2001
From: ao508 <15623749+ao508@users.noreply.github.com>
Date: Wed, 27 Dec 2023 10:52:40 -0500
Subject: [PATCH] Patient DMP ID lookup (#1070)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>
---
 .../org/mskcc/smile/model/SmilePatient.java    | 18 ++++++++++++++++++
 .../service/impl/CrdbMappingServiceImpl.java   |  4 +++-
 .../smile/service/impl/SampleServiceImpl.java  | 14 ++++++++++++++
 3 files changed, 35 insertions(+), 1 deletion(-)

diff --git a/model/src/main/java/org/mskcc/smile/model/SmilePatient.java b/model/src/main/java/org/mskcc/smile/model/SmilePatient.java
index 00240def..177c9b53 100644
--- a/model/src/main/java/org/mskcc/smile/model/SmilePatient.java
+++ b/model/src/main/java/org/mskcc/smile/model/SmilePatient.java
@@ -122,6 +122,24 @@ public Boolean hasPatientAlias(PatientAlias patientAlias) {
         return Boolean.FALSE;
     }
 
+    /**
+     * Determines whether Patient has a patient alias matching the namespace provided.
+     * @param patientAliasNamespace
+     * @return Boolean
+     */
+    public Boolean hasPatientAlias(String patientAliasNamespace) {
+        if (patientAliases == null) {
+            patientAliases = new ArrayList<>();
+            return Boolean.FALSE;
+        }
+        for (PatientAlias alias : patientAliases) {
+            if (alias.getNamespace().equalsIgnoreCase(patientAliasNamespace)) {
+                return Boolean.TRUE;
+            }
+        }
+        return Boolean.FALSE;
+    }
+
     @Override
     public String toString() {
         return ToStringBuilder.reflectionToString(this);
diff --git a/service/src/main/java/org/mskcc/smile/service/impl/CrdbMappingServiceImpl.java b/service/src/main/java/org/mskcc/smile/service/impl/CrdbMappingServiceImpl.java
index 31f1b938..a72d5a7f 100644
--- a/service/src/main/java/org/mskcc/smile/service/impl/CrdbMappingServiceImpl.java
+++ b/service/src/main/java/org/mskcc/smile/service/impl/CrdbMappingServiceImpl.java
@@ -67,7 +67,9 @@ public Object call() {
     @Override
     public CrdbMappingModel getCrdbMappingModelByInputId(String inputId) throws Exception {
         //Add check for if the input query starts with "C-" then remove it (replace with empty string)
-        inputId.replace("C-", "");
+        if (inputId.startsWith("C-")) {
+            inputId.replace("C-", "");
+        }
         Callable<Object> task = new Callable<Object>() {
             @Override
             public Object call() {
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
index aeb58114..baf71847 100644
--- a/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java
+++ b/service/src/main/java/org/mskcc/smile/service/impl/SampleServiceImpl.java
@@ -16,9 +16,11 @@
 import org.mskcc.smile.model.SmilePatient;
 import org.mskcc.smile.model.SmileRequest;
 import org.mskcc.smile.model.SmileSample;
+import org.mskcc.smile.model.internal.CrdbMappingModel;
 import org.mskcc.smile.model.web.PublishedSmileSample;
 import org.mskcc.smile.model.web.SmileSampleIdMapping;
 import org.mskcc.smile.persistence.neo4j.SmileSampleRepository;
+import org.mskcc.smile.service.CrdbMappingService;
 import org.mskcc.smile.service.SmilePatientService;
 import org.mskcc.smile.service.SmileRequestService;
 import org.mskcc.smile.service.SmileSampleService;
@@ -43,6 +45,10 @@ public class SampleServiceImpl implements SmileSampleService {
     @Autowired
     private SmilePatientService patientService;
 
+    @Autowired
+    private CrdbMappingService crdbMappingService;
+
+
     private static final Log LOG = LogFactory.getLog(SampleServiceImpl.class);
     private final ObjectMapper mapper = new ObjectMapper();
 
@@ -149,6 +155,14 @@ public SmileSample saveSmileSample(SmileSample
     public SmileSample fetchAndLoadPatientDetails(SmileSample sample) throws Exception {
         SampleMetadata sampleMetadata = sample.getLatestSampleMetadata();
         SmilePatient patient = sample.getPatient();
+        if (!patient.hasPatientAlias("dmpId")) {
+            CrdbMappingModel result =
+                    crdbMappingService.getCrdbMappingModelByInputId(patient.getCmoPatientId().getValue());
+            if (result != null) {
+                PatientAlias alias = new PatientAlias(result.getDmpId(), "dmpId");
+                patient.addPatientAlias(alias);
+            }
+        }
 
         // 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)