Standardize resolved sex val for research samples (#1641)

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

Author: ao508

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

@@ -66,6 +66,10 @@ public static SmileSample buildNewResearchSampleFromMetadata(String requestId,
         }
         sampleMetadata.setStatus(sampleStatus);
 
+        // standardize value for sex (M -> Male, F -> Female)
+        String sex = resolveIgoSampleSex(sampleMetadata.getSex());
+        sampleMetadata.setSex(sex);
+
         SmileSample sample = new SmileSample();
         sample.addSampleMetadata(sampleMetadata);
         sample.setSampleCategory("research");
@@ -143,6 +147,11 @@ public static SampleMetadata buildNewSampleMetadatafromJson(String sampleMetadat
                 mapper.readValue(sampleMetadataJson, SampleMetadata.class);
         sampleMetadata.setImportDate(
                 LocalDateTime.now().format(DateTimeFormatter.ISO_LOCAL_DATE));
+
+        // standardize value for sex (M -> Male, F -> Female)
+        String sex = resolveIgoSampleSex(sampleMetadata.getSex());
+        sampleMetadata.setSex(sex);
+
         // resolve igo request id if null from additionalProperties if possible
         if (sampleMetadata.getIgoRequestId() == null
                 && !sampleMetadata.getAdditionalProperties().isEmpty()) {
@@ -250,4 +259,16 @@ private static Status extractStatusFromJson(String inputJson)
         }
         return status;
     }
+
+    private static String resolveIgoSampleSex(String sex) {
+        // standardize value for sex (M -> Male, F -> Female)
+        if (!StringUtils.isBlank(sex)) {
+            return switch (sex.toUpperCase()) {
+                case "M" -> "Male";
+                case "F" -> "Female";
+                default -> sex;
+            };
+        }
+        return "";
+    }
 }

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

@@ -766,4 +766,14 @@ public void testNonCmoRequest() throws Exception {
             Assertions.assertNull(s.getSmilePatientId());
         }
     }
+
+    @Test
+    @Order(26)
+    public void testResolvedSampleSex() throws Exception {
+        String requestId = "MOCKREQUEST1_B";
+        String igoId = "MOCKREQUEST1_B_1";
+        SmileSample sample = sampleService.getResearchSampleByRequestAndIgoId(requestId, igoId);
+        SampleMetadata sm = sample.getLatestSampleMetadata();
+        Assertions.assertEquals("Female", sm.getSex());
+    }
 }