Issue 22 - Update to FHIR Ethnicity System (#23)

Signed-off-by: Brian Cragun <[email protected]> Signed-off-by: Brian Cragun <[email protected]> Co-authored-by: Brian Cragun <[email protected]>
LinuxForHealth · Aug 22, 2022 · 2dc1e5e · 2dc1e5e
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diff --git a/docs/datacontract.md b/docs/datacontract.md
@@ -89,7 +89,7 @@ The top-level key within a FileDefinition serves as the FileDefinition name. Thi
  "comment": "adds a default ethnic system code to the source data",
  "params": {
     "name": "ethnicitySystem",
-    "value": "http://terminology.hl7.org/CodeSystem/v2-0189"
+    "value": "http://terminology.hl7.org/CodeSystem/v3-Ethnicity"
  }
 }
 ```

diff --git a/docs/implementation-guide.md b/docs/implementation-guide.md
@@ -72,7 +72,7 @@ the parameters/arguments `name` and `value`:
           "name": "add_constant",
           "params": {
             "name": "ethnicitySystem",
-            "value": "http://terminology.hl7.org/CodeSystem/v2-0189"
+            "value": "http://terminology.hl7.org/CodeSystem/v3-Ethnicity"
           }
         },
       { etc }

diff --git a/src/linuxforhealth/csvtofhir/fhirutils/fhir_constants.py b/src/linuxforhealth/csvtofhir/fhirutils/fhir_constants.py
@@ -38,7 +38,7 @@ class SystemConstants:
     # FYI: Discharge Disposition HL7 standard uses numeric values "http://terminology.hl7.org/CodeSystem/v2-0112"
     DISCHARGE_DISPOSITION_SYSTEM = "http://terminology.hl7.org/CodeSystem/discharge-disposition"
     ENCOUNTER_CLASS_CODING_SYSTEM = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
-    ETHNICITY_SYSTEM = "http://terminology.hl7.org/CodeSystem/v2-0189"
+    ETHNICITY_SYSTEM = "http://terminology.hl7.org/CodeSystem/v3-Ethnicity"
     INCIDENT_CODE_SYSTEM = "http://terminology.hl7.org/CodeSystem/v3-ActCode"
     LOCATION_TYPE_SYSTEM = "http://terminology.hl7.org/CodeSystem/v3-RoleCode"
     MED_ADM_CATEGORY_SYSTEM = "http://terminology.hl7.org/CodeSystem/medication-admin-category"
@@ -299,8 +299,9 @@ class PatientResource:
         "2129-5": "Arab",
         "2131-1": "Other Race"
     }
-    ethnicity_display = {
-        "H": "Hispanic or Latino"
+    ethnicity_display = { #http://terminology.hl7.org/CodeSystem/v3-Ethnicity
+        "2135-2": "Hispanic or Latino",
+        "2186-5": "Not Hispanic or Latino"
     }
 
 

diff --git a/tests/fhirrs/test_patient.py b/tests/fhirrs/test_patient.py
@@ -136,9 +136,9 @@ def format_test_patient_record() -> Dict:
         "race": "UNK",
         "raceSystem": "http://terminology.hl7.org/CodeSystem/v3-NullFlavor",
         "raceText": "998",
-        "ethnicity": "H",
-        "ethnicitySystem": "urn:oid:2.16.840.1.113883.6.238",
-        "ethnicityText": "613",
+        "ethnicity": "2135-2",
+        "ethnicitySystem": "http://terminology.hl7.org/CodeSystem/v3-Ethnicity",
+        "ethnicityText": "Hispanic",
         "resourceType": "Patient",
         "deceasedBoolean": "False",
         "ageInWeeksForAgeUnder2Years": "69",
@@ -171,12 +171,12 @@ def format_test_patient_expected():
                 "valueCodeableConcept": {
                     "coding": [
                         {
-                            "system": "urn:oid:2.16.840.1.113883.6.238",
+                            "system": "http://terminology.hl7.org/CodeSystem/v3-Ethnicity",
                             "display": "Hispanic or Latino",
-                            "code": "H"
+                            "code": "2135-2"
                         }
                     ],
-                    "text": "613"
+                    "text": "Hispanic"
                 }
             },
             {

diff --git a/tests/model/test_patient_csv.py b/tests/model/test_patient_csv.py
@@ -39,4 +39,4 @@ def test_patient_system_defaults():
     }
     patient: PatientCsv = PatientCsv.parse_obj(pat_dictionary)
     patient.raceSystem = "http://terminology.hl7.org/CodeSystem/v3-Race"
-    patient.ethnicitySystem = "http://terminology.hl7.org/CodeSystem/v2-0189"
+    patient.ethnicitySystem = "http://terminology.hl7.org/CodeSystem/v3-Ethnicity"
diff --git a/tests/pipeline/test_tasks.py b/tests/pipeline/test_tasks.py
@@ -39,7 +39,7 @@ def test_add_constant(input_data_frame: DataFrame, expected_data_frame: DataFram
     :param expected_data_frame: The expected data frame, used for comparisons
     """
     expected_data_frame["ethnicitySystem"] = [
-        "http://terminology.hl7.org/CodeSystem/v2-0189"
+        "http://terminology.hl7.org/CodeSystem/v3-Ethnicity"
     ]
     expected_data_frame["raceSystem"] = [
         "http://terminology.hl7.org/CodeSystem/v3-Race"
@@ -48,7 +48,7 @@ def test_add_constant(input_data_frame: DataFrame, expected_data_frame: DataFram
     result: DataFrame = add_constant(
         input_data_frame,
         "ethnicitySystem",
-        "http://terminology.hl7.org/CodeSystem/v2-0189"
+        "http://terminology.hl7.org/CodeSystem/v3-Ethnicity"
     )
     result: DataFrame = add_constant(
         result, "raceSystem", "http://terminology.hl7.org/CodeSystem/v3-Race"