Map C-CDA Allergy Intolerance to FHIR Allergy Intolerance Category

chaseastewart · Feb 28, 2024 · c0f1873 · c0f1873
1 parent 760583f
commit c0f1873
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Showing 4 changed files with 64 additions and 43 deletions.
diff --git a/fhir_converter/filters.py b/fhir_converter/filters.py
@@ -247,11 +247,11 @@ def get_property(
     mapping = context.resolve("code_mapping", default={}).get(str_arg(mapping_key), None)
     if mapping:
         code_mapping = mapping.get(code, None)
-        if not code_mapping:
+        if not code_mapping or property not in code_mapping:
             code_mapping = mapping.get("__default__", {})
 
         mapped_code = code_mapping.get(property, None)
-        if mapped_code:
+        if mapped_code is not None:
             return mapped_code
 
     return code if property in ("code", "display") else ""

diff --git a/fhir_converter/templates/ccda/Resource/_AllergyIntolerance.liquid b/fhir_converter/templates/ccda/Resource/_AllergyIntolerance.liquid
@@ -20,6 +20,7 @@
                 }
             ]
         },
+        "category": "{{ allergyEntry.value.code | get_property: 'ValueSet/AllergyCategory' }}",
         "reaction":
         [
             {

diff --git a/fhir_converter/templates/ccda/ValueSet/ValueSet.json b/fhir_converter/templates/ccda/ValueSet/ValueSet.json
@@ -21,29 +21,23 @@
       }
     },
     "ValueSet/AllergyCategory": {
-      "416098002": {
-        "code": "medication"
-      },
-      "59037007": {
-        "code": "medication"
-      },
-      "419511003": {
-        "code": "medication"
+      "235719002": {
+        "code": "food"
       },
       "414285001": {
         "code": "food"
       },
-      "232347008": {
-        "code": "environment"
+      "418471000": {
+        "code": "food"
       },
-      "420134006": {
-        "code": "other"
+      "416098002": {
+        "code": "medication"
       },
-      "418038007": {
-        "code": "other"
+      "419511003": {
+        "code": "medication"
       },
-      "419199007": {
-        "code": "other"
+      "59037007": {
+        "code": "medication"
       },
       "__default__": {
         "code": ""

diff --git a/tests/test_filters.py b/tests/test_filters.py
@@ -477,7 +477,9 @@ class GetPropertTest(TestCase, FilterTest):
         "code_mapping": {
             "RequestStatus": {
                 "fatal": {"code": "severe", "display": "very severe"},
-                "retry": {"other": "retrying"},
+                "retry": {"other": "retrying", "code": "", "display": ""},
+                "unknown": {"other": ""},
+                "timeout": {},
                 "__default__": {
                     "code": "bad",
                     "display": "very bad",
@@ -494,78 +496,102 @@ def test_undefined(self) -> None:
         result = self.bound_template.render()
         self.assertEqual(result, "")
 
-    def test_undefined_property(self) -> None:
+    def test_undefined_valueset_code(self) -> None:
         result = self.bound_template.render(status="undefined", key="Undefined")
         self.assertEqual(result, "undefined")
 
-    def test_undefined_property_code(self) -> None:
-        result = self.bound_template.render(
-            status="undefined", key="Undefined", property="code"
-        )
-        self.assertEqual(result, "undefined")
-
-    def test_undefined_property_display(self) -> None:
+    def test_undefined_valueset_display(self) -> None:
         result = self.bound_template.render(
             status="undefined", key="Undefined", property="display"
         )
         self.assertEqual(result, "undefined")
 
-    def test_undefined_property_other(self) -> None:
+    def test_undefined_valueset_other(self) -> None:
         result = self.bound_template.render(
             status="undefined", key="Undefined", property="other"
         )
         self.assertEqual(result, "")
 
-    def test_default_property(self) -> None:
+    def test_valueset_default_code(self) -> None:
         result = self.bound_template.render(status="aborted", key="RequestStatus")
         self.assertEqual(result, "bad")
 
-    def test_default_property_code(self) -> None:
-        result = self.bound_template.render(
-            status="aborted", key="RequestStatus", property="code"
-        )
-        self.assertEqual(result, "bad")
-
-    def test_default_property_display(self) -> None:
+    def test_valueset_default_display(self) -> None:
         result = self.bound_template.render(
             status="aborted", key="RequestStatus", property="display"
         )
         self.assertEqual(result, "very bad")
 
-    def test_default_property_other(self) -> None:
+    def test_valueset_default_other(self) -> None:
         result = self.bound_template.render(
             status="aborted", key="RequestStatus", property="other"
         )
         self.assertEqual(result, "could be worse")
 
-    def test_default_property_undefined(self) -> None:
+    def test_valueset_undefined(self) -> None:
         result = self.bound_template.render(
             status="aborted", key="RequestStatus", property="undefined"
         )
         self.assertEqual(result, "")
 
-    def test_property(self) -> None:
+    def test_valueset_code(self) -> None:
         result = self.bound_template.render(status="fatal", key="RequestStatus")
         self.assertEqual(result, "severe")
 
-    def test_property_display(self) -> None:
+    def test_valueset_display(self) -> None:
         result = self.bound_template.render(
             status="fatal", key="RequestStatus", property="display"
         )
         self.assertEqual(result, "very severe")
 
-    def test_property_other(self) -> None:
+    def test_valueset_other(self) -> None:
         result = self.bound_template.render(
             status="retry", key="RequestStatus", property="other"
         )
         self.assertEqual(result, "retrying")
 
-    def test_property_undefined(self) -> None:
+    def test_valueset_code_blank(self) -> None:
+        result = self.bound_template.render(
+            status="retry", key="RequestStatus", property="code"
+        )
+        self.assertEqual(result, "")
+
+    def test_valueset_display_blank(self) -> None:
+        result = self.bound_template.render(
+            status="retry", key="RequestStatus", property="display"
+        )
+        self.assertEqual(result, "")
+
+    def test_valueset_other_blank(self) -> None:
         result = self.bound_template.render(
-            status="fatal", key="RequestStatus", property="other"
+            status="unknown", key="RequestStatus", property="other"
         )
         self.assertEqual(result, "")
 
+    def test_valueset_code_undefined_default(self) -> None:
+        result = self.bound_template.render(
+            status="unknown", key="RequestStatus", property="code"
+        )
+        self.assertEqual(result, "bad")
+
+    def test_valueset_display_undefined_default(self) -> None:
+        result = self.bound_template.render(
+            status="unknown", key="RequestStatus", property="display"
+        )
+        self.assertEqual(result, "very bad")
+
+    def test_valueset_empty_default_code(self) -> None:
+        result = self.bound_template.render(
+            status="timeout", key="RequestStatus", property="code"
+        )
+        self.assertEqual(result, "bad")
+
+    def test_valueset_empty_default_display(self) -> None:
+        result = self.bound_template.render(
+            status="timeout", key="RequestStatus", property="display"
+        )
+        self.assertEqual(result, "very bad")
+
 
 class GetFirstCcdaSectionsByTemplateIdTest(TestCase, FilterTest):
     template = """{{ msg | get_first_ccda_sections_by_template_id: template_ids }}"""
-Original file line number
+Diff line change
@@ Expand Up / @@ -20,6 +20,7 @@ @@
                     }
                 ]
             },
+            "category": "{{ allergyEntry.value.code | get_property: 'ValueSet/AllergyCategory' }}",
             "reaction":
             [
                 {
@@ Expand Down @@