Support dbGaP IRB consent protocol (#1776)

Add irbConsentProtocol as dbGaP property
Allow updates when submitted as part of a sample dbgap update message

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>

Author: ao508

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

@@ -17,11 +17,13 @@ public class DbGap implements Serializable {
     @Convert(UuidStringConverter.class)
     private UUID smileDbGapId;
     private String dbGapStudy;
+    private String irbConsentProtocol;
 
     public DbGap() {}
-    
+
     public DbGap(DbGapJson dbGapJson) {
         this.dbGapStudy = dbGapJson.getDbGapStudy();
+        this.irbConsentProtocol = dbGapJson.getIrbConsentProtocol();
     }
 
     /**
@@ -35,7 +37,7 @@ public DbGap(String dbGapStudy) {
     public UUID getSmileDgGapId() {
         return smileDbGapId;
     }
-    
+
     public void setSmileDgGapId(UUID smileDbGapId) {
         this.smileDbGapId = smileDbGapId;
     }
@@ -48,6 +50,14 @@ public void setDbGapStudy(String dbGapStudy) {
         this.dbGapStudy = dbGapStudy;
     }
 
+    public String getIrbConsentProtocol() {
+        return irbConsentProtocol;
+    }
+
+    public void setIrbConsentProtocol(String irbConsentProtocol) {
+        this.irbConsentProtocol = irbConsentProtocol;
+    }
+
     @Override
     public String toString() {
         return ToStringBuilder.reflectionToString(this);

model/src/main/java/org/mskcc/smile/model/json/DbGapJson.java

@@ -11,12 +11,21 @@ public class DbGapJson implements Serializable {
     private String primaryId;
     @JsonProperty("dbGapStudy")
     private String dbGapStudy;
+    @JsonProperty("irbConsentProtocol")
+    private String irbConsentProtocol;
 
     public DbGapJson() {}
 
-    public DbGapJson(String primaryId, String dbGapStudy) {
+    /**
+     * DbGapJson constructor.
+     * @param primaryId
+     * @param dbGapStudy
+     * @param irbConsentProtocol
+     */
+    public DbGapJson(String primaryId, String dbGapStudy, String irbConsentProtocol) {
         this.primaryId = primaryId;
         this.dbGapStudy = dbGapStudy;
+        this.irbConsentProtocol = irbConsentProtocol;
     }
 
     public String getPrimaryId() {
@@ -35,6 +44,14 @@ public void setDbGapStudy(String dbGapStudy) {
         this.dbGapStudy = dbGapStudy;
     }
 
+    public String getIrbConsentProtocol() {
+        return irbConsentProtocol;
+    }
+
+    public void setIrbConsentProtocol(String irbConsentProtocol) {
+        this.irbConsentProtocol = irbConsentProtocol;
+    }
+
     @Override
     public String toString() {
         return ToStringBuilder.reflectionToString(this);

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

@@ -26,7 +26,8 @@ public interface DbGapRepository extends Neo4jRepository<DbGap, UUID> {
     @Query("""
            MATCH (s: Sample)-[:HAS_METADATA]->(sm: SampleMetadata {primaryId: $dbGap.primaryId})
            MERGE (s)-[:HAS_DBGAP]->(d: DbGap)
-           SET d.dbGapStudy = $dbGap.dbGapStudy, d.smileDbGapId = $smileDbGapId
+           SET d.dbGapStudy = $dbGap.dbGapStudy, d.smileDbGapId = $smileDbGapId,
+           d.irbConsentProtocol = $dbGap.irbConsentProtocol
            RETURN DISTINCT d
            """)
     DbGap updateDbGap(@Param("smileDbGapId") UUID smileDbGapId, @Param("dbGap") DbGapJson dbGap);

service/src/test/java/org/mskcc/smile/service/DbGapServiceTest.java

@@ -122,16 +122,18 @@ public void testDbGapMerge() throws Exception {
         Assertions.assertTrue(sampleService.sampleExistsByInputId(samplePrimaryId));
 
         // now test save and fetch of dbgap node
-        DbGapJson dbGapJson = new DbGapJson(samplePrimaryId, "mockDbgapStudyId.v1");
+        DbGapJson dbGapJson = new DbGapJson(samplePrimaryId, "mockDbgapStudyId.v1", "IRB-123456");
         dbGapService.updateDbGap(dbGapJson);
         DbGap dbGapNode = dbGapService.getDbGapBySamplePrimaryId(samplePrimaryId);
         Assertions.assertEquals("mockDbgapStudyId.v1", dbGapNode.getDbGapStudy());
+        Assertions.assertEquals("IRB-123456", dbGapNode.getIrbConsentProtocol());
 
         //pretend that the dbgap study is updated to v2
-        DbGapJson dbGapJson2 = new DbGapJson(samplePrimaryId, "mockDbgapStudyId.v2");
+        DbGapJson dbGapJson2 = new DbGapJson(samplePrimaryId, "mockDbgapStudyId.v2", "IRB-123456");
         dbGapService.updateDbGap(dbGapJson2);
         DbGap dbGapNode2 = dbGapService.getDbGapBySamplePrimaryId(samplePrimaryId);
         Assertions.assertEquals("mockDbgapStudyId.v2", dbGapNode2.getDbGapStudy());
+        Assertions.assertEquals("IRB-123456", dbGapNode.getIrbConsentProtocol());
         Assertions.assertEquals(dbGapNode.getSmileDgGapId(), dbGapNode2.getSmileDgGapId());
     }
 }