Add recommended coverage to DMP additional properties (#1771)

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

Author: ao508

model/src/main/java/org/mskcc/smile/model/dmp/DmpSampleMetadata.java

@@ -93,6 +93,8 @@ public class DmpSampleMetadata {
     private String biopsySite;
     @JsonProperty("standard_coverage")
     private String standardCoverage;
+    @JsonProperty("recommended_coverage")
+    private String recommendedCoverage;
     @JsonIgnore
     private Map<String, Object> additionalProperties = new HashMap<String, Object>();
 
@@ -138,6 +140,7 @@ public DmpSampleMetadata() {}
      * @param wholeSlideViewerId
      * @param biopsySite
      * @param standardCoverage
+     * @param recommendedCoverage
      */
     public DmpSampleMetadata(Integer alys2sampleId, Integer cbxPatientId,
             Integer cbxSampleId, Integer ct, String dateTumorSequencing, String linkedMskimpactCase,
@@ -152,7 +155,7 @@ public DmpSampleMetadata(Integer alys2sampleId, Integer cbxPatientId,
             Double tmbScore, Double tmbTtPercentile, String tumorPurity,
             String tumorTypeCode, String tumorTypeName,
             String consentPartA, String consentPartC, String wholeSlideViewerId,
-            String biopsySite, String standardCoverage) {
+            String biopsySite, String standardCoverage, String recommendedCoverage) {
         this.alys2sampleId = alys2sampleId;
         this.cbxPatientId = cbxPatientId;
         this.cbxSampleId = cbxSampleId;
@@ -191,6 +194,7 @@ public DmpSampleMetadata(Integer alys2sampleId, Integer cbxPatientId,
         this.wholeSlideViewerId = wholeSlideViewerId;
         this.biopsySite = biopsySite;
         this.standardCoverage = standardCoverage;
+        this.recommendedCoverage = recommendedCoverage;
     }
 
     public String getSomaticStatus() {
@@ -497,6 +501,14 @@ public void setStandardCoverage(String standardCoverage) {
         this.standardCoverage = standardCoverage;
     }
 
+    public String getRecommendedCoverage() {
+        return recommendedCoverage;
+    }
+
+    public void setRecommendedCoverage(String recommendedCoverage) {
+        this.recommendedCoverage = recommendedCoverage;
+    }
+
     public Map<String, Object> getAdditionalProperties() {
         return this.additionalProperties;
     }

service/src/main/java/org/mskcc/smile/service/util/SampleDataFactory.java

@@ -186,25 +186,51 @@ 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",
-                dmpSampleMetadata.getMsiScore());
-        sampleMetadata.addAdditionalProperty("msi-type",
-                dmpSampleMetadata.getMsiType());
-        sampleMetadata.addAdditionalProperty("consent-parta",
-                dmpSampleMetadata.getConsentPartA());
-        sampleMetadata.addAdditionalProperty("consent-partc",
-                dmpSampleMetadata.getConsentPartC());
-        sampleMetadata.addAdditionalProperty("tmb_cohort_percentile",
-                String.valueOf(dmpSampleMetadata.getTmbCohortPercentile()));
-        sampleMetadata.addAdditionalProperty("tmb_score",
-                String.valueOf(dmpSampleMetadata.getTmbScore()));
-        sampleMetadata.addAdditionalProperty("tmb_tt_percentile",
-                String.valueOf(dmpSampleMetadata.getTmbTtPercentile()));
-        sampleMetadata.addAdditionalProperty("standard_coverage",
-                dmpSampleMetadata.getStandardCoverage());
+
+        // conditionally set additional properties
+        if (dmpSampleMetadata.getCt() != null) {
+            sampleMetadata.addAdditionalProperty("ct", String.valueOf(dmpSampleMetadata.getCt()));
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getMsiComment())) {
+            sampleMetadata.addAdditionalProperty("msi-comment",
+                    dmpSampleMetadata.getMsiComment());
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getMsiScore())) {
+            sampleMetadata.addAdditionalProperty("msi-score",
+                    dmpSampleMetadata.getMsiScore());
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getMsiType())) {
+            sampleMetadata.addAdditionalProperty("msi-type",
+                    dmpSampleMetadata.getMsiType());
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getConsentPartA())) {
+            sampleMetadata.addAdditionalProperty("consent-parta",
+                    dmpSampleMetadata.getConsentPartA());
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getConsentPartC())) {
+            sampleMetadata.addAdditionalProperty("consent-partc",
+                    dmpSampleMetadata.getConsentPartC());
+        }
+        if (dmpSampleMetadata.getTmbCohortPercentile() != null) {
+            sampleMetadata.addAdditionalProperty("tmb_cohort_percentile",
+                    String.valueOf(dmpSampleMetadata.getTmbCohortPercentile()));
+        }
+        if (dmpSampleMetadata.getTmbScore() != null) {
+            sampleMetadata.addAdditionalProperty("tmb_score",
+                    String.valueOf(dmpSampleMetadata.getTmbScore()));
+        }
+        if (dmpSampleMetadata.getTmbTtPercentile() != null) {
+            sampleMetadata.addAdditionalProperty("tmb_tt_percentile",
+                    String.valueOf(dmpSampleMetadata.getTmbTtPercentile()));
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getStandardCoverage())) {
+            sampleMetadata.addAdditionalProperty("standard_coverage",
+                    dmpSampleMetadata.getStandardCoverage());
+        }
+        if (!StringUtils.isBlank(dmpSampleMetadata.getRecommendedCoverage())) {
+            sampleMetadata.addAdditionalProperty("recommended_coverage",
+                    dmpSampleMetadata.getRecommendedCoverage());
+        }
         return sampleMetadata;
     }