From fa6063431e23789c11d6dc132028e667884797e5 Mon Sep 17 00:00:00 2001
From: jeffquinn-msk <quinnj2@mskcc.org>
Date: Wed, 26 Jul 2023 13:50:41 -0400
Subject: [PATCH] Pass through from annotation to API

---
 .../component/annotation/OncokbResolver.java      |  5 +++--
 .../cbioportal/genome_nexus/model/Alteration.java | 15 ++++++++++++++-
 .../service/internal/OncokbServiceImpl.java       |  6 ++++--
 3 files changed, 21 insertions(+), 5 deletions(-)

diff --git a/component/src/main/java/org/cbioportal/genome_nexus/component/annotation/OncokbResolver.java b/component/src/main/java/org/cbioportal/genome_nexus/component/annotation/OncokbResolver.java
index eac00eae2..8ef1717f1 100644
--- a/component/src/main/java/org/cbioportal/genome_nexus/component/annotation/OncokbResolver.java
+++ b/component/src/main/java/org/cbioportal/genome_nexus/component/annotation/OncokbResolver.java
@@ -24,7 +24,8 @@ public Alteration resolve(VariantAnnotationSummary annotationSummary)
                                             transcriptConsequenceSummary.getProteinPosition() != null ? transcriptConsequenceSummary.getProteinPosition().getStart() : null,
                                             transcriptConsequenceSummary.getProteinPosition() != null ? transcriptConsequenceSummary.getProteinPosition().getEnd() : null,
                                             // TODO tumorType is optional for the query, currently genome nexus doesn't have tumorType data
-                                            null);
+                                            null,
+                                            annotationSummary.getAssemblyName());
             }
         }
 
@@ -37,4 +38,4 @@ private String normalizeProteinChange(String proteinChange) {
         }
         return proteinChange;
     }
-}
\ No newline at end of file
+}
diff --git a/model/src/main/java/org/cbioportal/genome_nexus/model/Alteration.java b/model/src/main/java/org/cbioportal/genome_nexus/model/Alteration.java
index d75cbbc63..b0d31d50a 100644
--- a/model/src/main/java/org/cbioportal/genome_nexus/model/Alteration.java
+++ b/model/src/main/java/org/cbioportal/genome_nexus/model/Alteration.java
@@ -25,8 +25,12 @@ public class Alteration
     @Field(value = "tumorType")
     private String tumorType;
 
+    @Field(value = "referenceAssembly")
+    private String referenceAssembly;
+
     public Alteration(String hugoSymbol, Integer entrezGeneId, String alteration,
-                        String consequence, Integer proteinStart, Integer proteinEnd, String tumorType)
+                      String consequence, Integer proteinStart, Integer proteinEnd, String tumorType,
+                      String referenceAssembly)
     {
         this.hugoSymbol = hugoSymbol;
         this.entrezGeneId = entrezGeneId;
@@ -35,6 +39,7 @@ public Alteration(String hugoSymbol, Integer entrezGeneId, String alteration,
         this.proteinStart = proteinStart;
         this.proteinEnd = proteinEnd;
         this.tumorType = tumorType;
+        this.referenceAssembly = referenceAssembly;
     }
 
     public String getHugoSymbol() {
@@ -92,4 +97,12 @@ public String getTumorType() {
     public void setTumorType(String tumorType) {
         this.tumorType = tumorType;
     }
+
+    public String getReferenceAssembly() {
+        return referenceAssembly;
+    }
+
+    public void setReferenceAssembly(String referenceAssembly) {
+        this.referenceAssembly = referenceAssembly;
+    }
 }
diff --git a/service/src/main/java/org/cbioportal/genome_nexus/service/internal/OncokbServiceImpl.java b/service/src/main/java/org/cbioportal/genome_nexus/service/internal/OncokbServiceImpl.java
index f1b56c4ce..a0c54fd37 100644
--- a/service/src/main/java/org/cbioportal/genome_nexus/service/internal/OncokbServiceImpl.java
+++ b/service/src/main/java/org/cbioportal/genome_nexus/service/internal/OncokbServiceImpl.java
@@ -36,7 +36,7 @@ public OncokbServiceImpl(OncokbDataFetcher oncokbDataFetcher, OncokbCancerGenesL
 
     public IndicatorQueryResp getOncokbByProteinChange(Alteration alteration, String token) throws OncokbNotFoundException, OncokbWebServiceException {
         Optional<IndicatorQueryResp> oncokb = null;
-        
+
         oncokbDataFetcher.setOncokbToken(token);
         try {
             // get the annotation from the web service
@@ -96,6 +96,8 @@ private String generateQueryString(Alteration alteration) {
         if (alteration.getTumorType() != null) {
             query = query + "&tumorType=" + alteration.getTumorType();
         }
+        query = query + "&referenceGenome=" + alteration.getReferenceAssembly();
+
         // TODO tumorType is optional for the query, currently genome nexus doesn't have tumorType data
 
         return query;
@@ -104,4 +106,4 @@ private String generateQueryString(Alteration alteration) {
     public List<CancerGene> getOncokbCancerGenesList() {
         return this.oncokbCancerGenesListRepository.getOncokbCancerGenesList();
     }
-}
\ No newline at end of file
+}