From 76d139165d068d7cc415560ffdfe226ae2f45cfd Mon Sep 17 00:00:00 2001
From: ao508 <15623749+ao508@users.noreply.github.com>
Date: Thu, 18 Jul 2024 13:40:25 -0400
Subject: [PATCH] DMP model update - support 'ct' json property (#1228)

Signed-off-by: Angelica Ochoa <15623749+ao508@users.noreply.github.com>
---
 .../mskcc/smile/model/dmp/DmpSampleMetadata.java   | 14 +++++++++++++-
 .../smile/service/util/SampleDataFactory.java      |  1 +
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/model/src/main/java/org/mskcc/smile/model/dmp/DmpSampleMetadata.java b/model/src/main/java/org/mskcc/smile/model/dmp/DmpSampleMetadata.java
index eec3373d..c54ba67b 100644
--- a/model/src/main/java/org/mskcc/smile/model/dmp/DmpSampleMetadata.java
+++ b/model/src/main/java/org/mskcc/smile/model/dmp/DmpSampleMetadata.java
@@ -23,6 +23,8 @@ public class DmpSampleMetadata {
     private Integer cbxPatientId;
     @JsonProperty("cbx_sample_id")
     private Integer cbxSampleId;
+    @JsonProperty("ct")
+    private Integer ct;
     @JsonProperty("date_tumor_sequencing")
     private String dateTumorSequencing;
     @JsonProperty("linked_mskimpact_case")
@@ -101,6 +103,7 @@ public DmpSampleMetadata() {}
      * @param alys2sampleId
      * @param cbxPatientId
      * @param cbxSampleId
+     * @param ct
      * @param dateTumorSequencing
      * @param linkedMskimpactCase
      * @param dmpAlysTaskId
@@ -137,7 +140,7 @@ public DmpSampleMetadata() {}
      * @param standardCoverage
      */
     public DmpSampleMetadata(Integer alys2sampleId, Integer cbxPatientId,
-            Integer cbxSampleId, String dateTumorSequencing, String linkedMskimpactCase,
+            Integer cbxSampleId, Integer ct, String dateTumorSequencing, String linkedMskimpactCase,
             Integer dmpAlysTaskId, String dmpAlysTaskName, String dmpPatientId,
             String dmpSampleId, Integer dmpSampleSoId, Integer gender,
             String genePanel, Integer isMetastasis, String legacyPatientId,
@@ -153,6 +156,7 @@ public DmpSampleMetadata(Integer alys2sampleId, Integer cbxPatientId,
         this.alys2sampleId = alys2sampleId;
         this.cbxPatientId = cbxPatientId;
         this.cbxSampleId = cbxSampleId;
+        this.ct = ct;
         this.dateTumorSequencing = dateTumorSequencing;
         this.dmpAlysTaskId = dmpAlysTaskId;
         this.dmpAlysTaskName = dmpAlysTaskName;
@@ -221,6 +225,14 @@ public void setCbxSampleId(Integer cbxSampleId) {
         this.cbxSampleId = cbxSampleId;
     }
 
+    public Integer getCt() {
+        return ct;
+    }
+
+    public void setCt(Integer ct) {
+        this.ct = ct;
+    }
+
     public String getDateTumorSequencing() {
         return dateTumorSequencing;
     }
diff --git a/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java b/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java
index a1cbf651..938af6bc 100644
--- a/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java
+++ b/service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java
@@ -166,6 +166,7 @@ public static SampleMetadata buildNewSampleMetadataFromDmpSample(String cmoPatie
                 resolveDmpSampleClass(dmpSampleMetadata.getDmpSampleId()));
         sampleMetadata.setSampleType(
                 resolveDmpSampleType(dmpSampleMetadata.getIsMetastasis()));
+        sampleMetadata.addAdditionalProperty("ct", String.valueOf(dmpSampleMetadata.getCt()));
         sampleMetadata.addAdditionalProperty("msi-comment",
                 dmpSampleMetadata.getMsiComment());
         sampleMetadata.addAdditionalProperty("msi-score",