Add conclusionCode to diagnosticreport table

smart-on-fhir · Dec 4, 2024 · 0c01575 · 0c01575
1 parent 47c8e3e
commit 0c01575
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Showing 5 changed files with 70 additions and 3 deletions.
diff --git a/cumulus_library/studies/core/builder_diagnosticreport.py b/cumulus_library/studies/core/builder_diagnosticreport.py
@@ -31,6 +31,11 @@ def prepare_queries(self, *args, config: cumulus_library.StudyConfig, **kwargs):
                 column_hierarchy=[("code", dict)],
                 target_table="core__diagnosticreport_dn_code",
             ),
+            sql_utils.CodeableConceptConfig(
+                source_table="diagnosticreport",
+                column_hierarchy=[("conclusionCode", list)],
+                target_table="core__diagnosticreport_dn_conclusioncode",
+            ),
         ]
         self.queries += sql_utils.denormalize_complex_objects(config.db, code_sources)
         validated_schema = sql_utils.validate_schema(config.db, expected_table_cols)

diff --git a/cumulus_library/studies/core/core_templates/diagnosticreport.sql.jinja b/cumulus_library/studies/core/core_templates/diagnosticreport.sql.jinja
@@ -7,6 +7,9 @@
 -- * the `reporter` field, simply due to it not likely being interesting to consumers
 --   and being an array field, which would require a lot of row duplication.
 --
+-- AND ADDING:
+-- * the `conclusionCode` field, because it has clinical relevance
+--
 -- US Core profiles for reference:
 -- * https://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-diagnosticreport-lab.html
 -- * https://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-diagnosticreport-note.html
@@ -91,6 +94,10 @@ SELECT
     td.issued_month,
     td.issued_year,
 
+    dn_conclusion.code AS conclusionCode_code,
+    dn_conclusion.system AS conclusionCode_system,
+    dn_conclusion.display AS conclusionCode_display,
+
     concat('DiagnosticReport/', td.id) AS diagnosticreport_ref,
     td.subject_ref,
     td.encounter_ref,
@@ -99,4 +106,6 @@ SELECT
 FROM temp_diagnosticreport AS td
 LEFT JOIN core__diagnosticreport_dn_code AS dn_code ON td.id = dn_code.id
 LEFT JOIN core__diagnosticreport_dn_category AS dn_category ON td.id = dn_category.id
+LEFT JOIN core__diagnosticreport_dn_conclusioncode AS dn_conclusion
+    ON td.id = dn_conclusion.id
 LEFT JOIN temp_result AS tr ON td.id = tr.id;
diff --git a/cumulus_library/studies/core/reference_sql/builder_diagnosticreport.sql b/cumulus_library/studies/core/reference_sql/builder_diagnosticreport.sql
@@ -95,6 +95,18 @@ CREATE TABLE core__diagnosticreport_dn_code AS (
 
 -- ###########################################################
 
+CREATE TABLE IF NOT EXISTS "main"."core__diagnosticreport_dn_conclusioncode"
+AS (
+    SELECT * FROM (
+        VALUES
+        (cast(NULL AS varchar),cast(NULL AS bigint),cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS varchar),cast(NULL AS boolean))
+    )
+        AS t ("id","row","code","system","display","userSelected")
+    WHERE 1 = 0 -- ensure empty table
+);
+
+-- ###########################################################
+
 
 
 
@@ -104,6 +116,9 @@ CREATE TABLE core__diagnosticreport_dn_code AS (
 -- * the `reporter` field, simply due to it not likely being interesting to consumers
 --   and being an array field, which would require a lot of row duplication.
 --
+-- AND ADDING:
+-- * the `conclusionCode` field, because it has clinical relevance
+--
 -- US Core profiles for reference:
 -- * https://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-diagnosticreport-lab.html
 -- * https://hl7.org/fhir/us/core/STU4/StructureDefinition-us-core-diagnosticreport-note.html
@@ -192,6 +207,10 @@ SELECT
     td.issued_month,
     td.issued_year,
 
+    dn_conclusion.code AS conclusionCode_code,
+    dn_conclusion.system AS conclusionCode_system,
+    dn_conclusion.display AS conclusionCode_display,
+
     concat('DiagnosticReport/', td.id) AS diagnosticreport_ref,
     td.subject_ref,
     td.encounter_ref,
@@ -200,4 +219,6 @@ SELECT
 FROM temp_diagnosticreport AS td
 LEFT JOIN core__diagnosticreport_dn_code AS dn_code ON td.id = dn_code.id
 LEFT JOIN core__diagnosticreport_dn_category AS dn_category ON td.id = dn_category.id
+LEFT JOIN core__diagnosticreport_dn_conclusioncode AS dn_conclusion
+    ON td.id = dn_conclusion.id
 LEFT JOIN temp_result AS tr ON td.id = tr.id;
diff --git a/docs/core-study-details.md b/docs/core-study-details.md
@@ -82,6 +82,8 @@ Per resource, the optional fields are as follows:
 - Condition
   - encounter
   - recordedDate
+- DiagnosticReport
+  - conclusionCode
 - DocumentReference
   - docStatus
 - Encounter
@@ -408,6 +410,18 @@ vital signs) instead.
 |userselected|boolean|           |
 
 
+### core__diagnosticreport_dn_conclusioncode
+
+|   Column   | Type  |Description|
+|------------|-------|-----------|
+|id          |varchar|           |
+|row         |bigint |           |
+|code        |varchar|           |
+|system      |varchar|           |
+|display     |varchar|           |
+|userselected|boolean|           |
+
+
 ### core__documentreference
 
 |       Column        | Type  |Description|

diff --git a/tests/core/test_core_diagreports.py b/tests/core/test_core_diagreports.py
@@ -42,13 +42,16 @@ def test_core_diag_report_many_cases(tmp_path):
             {"reference": "Observation/result1"},
             {"reference": "Observation/result2"},
         ],
+        conclusionCode=[
+            {"coding": [{"code": "conc1", "system": "sys:conc", "display": "Conclusion One"}]},
+            {"coding": [{"code": "conc2", "system": "sys:conc", "display": "Conclusion Two"}]},
+        ],
     )
 
     con = testbed.build()
     df = con.sql("SELECT * FROM core__diagnosticreport").df()
     rows = json.loads(df.to_json(orient="records"))
-
-    assert 8 == len(rows)
+    assert len(rows) == 16
 
     combos = combine_dictionaries(
         # Start with a list of size one - all the consistent elements across all rows
@@ -85,12 +88,24 @@ def test_core_diag_report_many_cases(tmp_path):
             {"code_code": "code1", "code_system": "sys:code", "code_display": "Code One"},
             {"code_code": "code2", "code_system": "sys:code", "code_display": "Code Two"},
         ],
+        [
+            {
+                "conclusionCode_code": "conc1",
+                "conclusionCode_system": "sys:conc",
+                "conclusionCode_display": "Conclusion One",
+            },
+            {
+                "conclusionCode_code": "conc2",
+                "conclusionCode_system": "sys:conc",
+                "conclusionCode_display": "Conclusion Two",
+            },
+        ],
         [
             {"result_ref": "Observation/result1"},
             {"result_ref": "Observation/result2"},
         ],
     )
-    assert 8 == len(combos)  # sanity check our product math
+    assert len(combos) == 16  # sanity check our product math
 
     assert dict_set_from_list(rows) == dict_set_from_list(combos)
 
@@ -134,6 +149,9 @@ def test_core_diag_report_minimal(tmp_path):
             "issued_month": None,
             "issued_year": None,
             "result_ref": None,
+            "conclusionCode_code": None,
+            "conclusionCode_system": None,
+            "conclusionCode_display": None,
         }
     ]