discovery cleanup

smart-on-fhir · Mar 21, 2024 · 81ad97a · 81ad97a
1 parent f965d00
commit 81ad97a
Show file tree

Hide file tree

Showing 3 changed files with 46 additions and 19 deletions.
diff --git a/cumulus_library/studies/discovery/code_detection.py b/cumulus_library/studies/discovery/code_detection.py
@@ -15,8 +15,8 @@ def _check_coding_against_db(self, code_source, schema, cursor):
             return sql_utils.is_field_populated(
                 schema=schema,
                 source_table=code_source["table_name"],
-                hierarchy=[(code_source["column_name"], list), ("coding", list)],
-                expected=[code_source["column_name"], *sql_utils.CODING],
+                hierarchy=[(code_source["column_name"], list)],
+                expected=sql_utils.CODEABLE_CONCEPT,
                 cursor=cursor,
             )
         elif code_source["is_bare_coding"]:
@@ -30,8 +30,8 @@ def _check_coding_against_db(self, code_source, schema, cursor):
         return sql_utils.is_field_populated(
             schema=schema,
             source_table=code_source["table_name"],
-            hierarchy=[(code_source["column_name"], dict), ("coding", list)],
-            expected=[code_source["column_name"], *sql_utils.CODING],
+            hierarchy=[(code_source["column_name"], dict)],
+            expected=sql_utils.CODEABLE_CONCEPT,
             cursor=cursor,
         )
 

diff --git a/tests/test_data/discovery/discovery__code_sources.txt b/tests/test_data/discovery/discovery__code_sources.txt
@@ -1,4 +1,4 @@
-condition,category,,,
+condition,category,encounter-diagnosis,Encounter Diagnosis,http://terminology.hl7.org/CodeSystem/condition-category
 condition,code,10509002,Acute bronchitis (disorder),http://snomed.info/sct
 condition,code,160903007,Full-time employment (finding),http://snomed.info/sct
 condition,code,195662009,Acute viral pharyngitis (disorder),http://snomed.info/sct
@@ -10,21 +10,48 @@ condition,code,44465007,Sprain of ankle,http://snomed.info/sct
 condition,code,444814009,Viral sinusitis (disorder),http://snomed.info/sct
 condition,code,73595000,Stress (finding),http://snomed.info/sct
 condition,code,741062008,Not in labor force (finding),http://snomed.info/sct
-documentreference,category,,,
-documentreference,type,,,
+documentreference,category,clinical-note,Clinical Note,http://hl7.org/fhir/us/core/CodeSystem/us-core-documentreference-category
+documentreference,type,34111-5,Emergency department note,http://loinc.org
+documentreference,type,51847-2,Evaluation + Plan note,http://loinc.org
 encounter,class,AMB,None,http://terminology.hl7.org/CodeSystem/v3-ActCode
 encounter,class,EMER,None,http://terminology.hl7.org/CodeSystem/v3-ActCode
 encounter,hospitalization.dischargedisposition,,,
 encounter,priority,,,
-encounter,reasoncode,,,
+encounter,reasoncode,10509002,Acute bronchitis (disorder),http://snomed.info/sct
+encounter,reasoncode,161665007,History of renal transplant (situation),http://snomed.info/sct
+encounter,reasoncode,195662009,Acute viral pharyngitis (disorder),http://snomed.info/sct
+encounter,reasoncode,271737000,Anemia (disorder),http://snomed.info/sct
+encounter,reasoncode,431857002,Chronic kidney disease stage 4 (disorder),http://snomed.info/sct
+encounter,reasoncode,444814009,Viral sinusitis (disorder),http://snomed.info/sct
+encounter,reasoncode,55680006,Drug overdose,http://snomed.info/sct
+encounter,reasoncode,72892002,Normal pregnancy,http://snomed.info/sct
+encounter,reasoncode,88805009,Chronic congestive heart failure (disorder),http://snomed.info/sct
 encounter,servicetype,,,
-encounter,type,,,
+encounter,type,162673000,General examination of patient (procedure),http://snomed.info/sct
+encounter,type,185345009,Encounter for symptom,http://snomed.info/sct
+encounter,type,185347001,Encounter for problem,http://snomed.info/sct
+encounter,type,185347001,Encounter for problem (procedure),http://snomed.info/sct
+encounter,type,185349003,Encounter for check up,http://snomed.info/sct
+encounter,type,185349003,Encounter for check up (procedure),http://snomed.info/sct
+encounter,type,308335008,Patient encounter procedure,http://snomed.info/sct
+encounter,type,371883000,Outpatient procedure,http://snomed.info/sct
+encounter,type,410620009,Well child visit (procedure),http://snomed.info/sct
+encounter,type,424619006,Prenatal visit,http://snomed.info/sct
+encounter,type,439740005,Postoperative follow-up visit (procedure),http://snomed.info/sct
+encounter,type,448337001,Telemedicine consultation with patient,http://snomed.info/sct
+encounter,type,50849002,Emergency room admission (procedure),http://snomed.info/sct
+encounter,type,698314001,Consultation for treatment,http://snomed.info/sct
+encounter,type,702927004,Urgent care clinic (environment),http://snomed.info/sct
 medication,codecodeableconcept ,,,
 medication,medicationcode,,,
-observation,category,,,
+observation,category,laboratory,Laboratory,http://terminology.hl7.org/CodeSystem/observation-category
 observation,code,34533-0,Odor of Urine,http://loinc.org
 observation,code,5778-6,Color of Urine,http://loinc.org
 observation,dataabsentreason,,,
 observation,interpretation,,,
-observation,valuecodeableconcept,,,
-patient,maritalstatus,,,
+observation,valuecodeableconcept,167248002,Urine smell ammoniacal (finding),http://snomed.info/sct
+observation,valuecodeableconcept,371254008,Brown color (qualifier value),http://snomed.info/sct
+patient,maritalstatus,D,Divorced,http://terminology.hl7.org/CodeSystem/v3-MaritalStatus
+patient,maritalstatus,M,Married,http://terminology.hl7.org/CodeSystem/v3-MaritalStatus
+patient,maritalstatus,S,Never Married,http://terminology.hl7.org/CodeSystem/v3-MaritalStatus
+patient,maritalstatus,W,Widowed,http://terminology.hl7.org/CodeSystem/v3-MaritalStatus
diff --git a/tests/test_discovery.py b/tests/test_discovery.py
@@ -44,13 +44,13 @@ def test_discovery(tmp_path):
     table_rows = conftest.get_sorted_table_data(cursor, "discovery__code_sources")
 
     # For regenerating test data
-    with open(
-        f"{pathlib.Path(__file__).resolve().parents[0]}"
-        "/test_data/discovery/discovery__code_sources.txt",
-        "w",
-    ) as f:
-        for row in table_rows:
-            f.write(f"{','.join(str(x) for x in row)}\n")
+    # with open(
+    #     f"{pathlib.Path(__file__).resolve().parents[0]}"
+    #     "/test_data/discovery/discovery__code_sources.txt",
+    #     "w",
+    # ) as f:
+    #     for row in table_rows:
+    #         f.write(f"{','.join(str(x) for x in row)}\n")
 
     with open(
         f"{pathlib.Path(__file__).resolve().parents[0]}"