Merge pull request #45 from smart-on-fhir/mikix/system-tweaks

q_system_use: update to match new qualifier guidance

README.md

@@ -4,7 +4,7 @@ A Cumulus-based implementation of the [qualifier metrics](https://github.com/syn
 
 ## Implemented Metrics
 
-The following qualifier metrics are implemented (per May 2024 qualifer definitions).
+The following qualifier metrics are implemented (per June 2024 qualifer definitions).
 
 - [c_pt_count](https://github.com/sync-for-science/qualifier/blob/master/metrics.md#c_pt_count)
 - [c_pt_deceased_count](https://github.com/sync-for-science/qualifier/blob/master/metrics.md#c_pt_deceased_count)

cumulus_library_data_metrics/q_system_use/q_system_use.jinja

@@ -36,6 +36,9 @@ SELECT
     {{ field }}
 FROM rejoined_src
 WHERE
-    has_target_system IS NULL
-    OR NOT has_target_system
+    {{ field }} IS NOT NULL
+    AND (
+        has_target_system IS NULL
+        OR NOT has_target_system
+    )
 );

cumulus_library_data_metrics/q_system_use/q_system_use.py

@@ -29,7 +29,9 @@ def add_metric_queries(self) -> None:
         )
         self.make_table(src="Device", field="type", systems=[systems.SNOMED])
         self.make_table(src="DiagnosticReport", field="code", systems=[systems.LOINC])
-        self.make_table(src="DocumentReference", field="type", systems=[systems.LOINC])
+        self.make_table(
+            src="DocumentReference", field="type", systems=[systems.LOINC, systems.NULL_FLAVOR]
+        )
         self.make_table(
             src="Immunization",
             field="vaccineCode",
@@ -68,8 +70,8 @@ def add_metric_queries(self) -> None:
                 systems.CPT,
                 systems.LOINC,
                 systems.SNOMED,
-                "http://ada.org/cdt",
-                "http://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets",
+                "http://www.ada.org/cdt",
+                "https://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets",
                 "http://www.cms.gov/Medicare/Coding/ICD10",
             ],
         )

cumulus_library_data_metrics/systems.py

@@ -6,6 +6,7 @@
 ICD10CM = "http://hl7.org/fhir/sid/icd-10-cm"
 LOINC = "http://loinc.org"
 NDC = "http://hl7.org/fhir/sid/ndc"
+NULL_FLAVOR = "http://terminology.hl7.org/CodeSystem/v3-NullFlavor"
 RXNORM = "http://www.nlm.nih.gov/research/umls/rxnorm"
 SNOMED = "http://snomed.info/sct"
 UCUM = "http://unitsofmeasure.org"

tests/data/q_system_use/general/documentreference/0.ndjson

@@ -1 +1,3 @@
-{"id": "valid", "type": {"coding":  [{"system": "http://loinc.org"}]}}
+{"id": "valid-loinc", "type": {"coding":  [{"system": "http://loinc.org"}]}}
+{"id": "valid-null", "type": {"coding":  [{"system": "http://terminology.hl7.org/CodeSystem/v3-NullFlavor"}]}}
+{"id": "invalid", "type": {"coding":  [{"system": "http://snomed.info/sct"}]}}

tests/data/q_system_use/general/expected_summary.csv

@@ -1,13 +1,13 @@
 id,numerator,denominator,percentage
 # Various edge cases here in procedure
-procedure_code,5,7,71.43
-# Rest are just short happy-path checks to confirm that we look at the right json field
-observation_valuecodeableconcept,1,2,50.00
-observation_code,1,2,50.00
+procedure_code,4,12,33.33
+# Rest are often short happy-path checks to confirm that we look at the right json field
+observation_valuecodeableconcept,0,2,0.00
+observation_code,0,2,0.00
 medicationrequest_medicationcodeableconcept,0,1,0.00
 medication_code,0,1,0.00
 immunization_vaccinecode,0,1,0.00
-documentreference_type,0,1,0.00
+documentreference_type,1,3,33.33
 diagnosticreport_code,0,1,0.00
 device_type,0,1,0.00
 condition_code,0,1,0.00

tests/data/q_system_use/general/procedure/0.ndjson

@@ -1,4 +1,9 @@
-{"id": "valid-simple", "code": {"coding": [{"system": "http://www.ama-assn.org/go/cpt"}]}}
+{"id": "valid-cdt", "code": {"coding": [{"system": "http://www.ada.org/cdt"}]}}
+{"id": "valid-cpt", "code": {"coding": [{"system": "http://www.ama-assn.org/go/cpt"}]}}
+{"id": "valid-hcpcs", "code": {"coding": [{"system": "https://www.cms.gov/Medicare/Coding/HCPCSReleaseCodeSets"}]}}
+{"id": "valid-icd10", "code": {"coding": [{"system": "http://www.cms.gov/Medicare/Coding/ICD10"}]}}
+{"id": "valid-loinc", "code": {"coding": [{"system": "http://loinc.org"}]}}
+{"id": "valid-snomed", "code": {"coding": [{"system": "http://snomed.info/sct"}]}}
 {"id": "valid-multiple", "code": {"coding": [{"system": "nope"}, {"system": "http://loinc.org"}]}}
 {"id": "bad-system", "code": {"coding": [{"system": "nope"}]}}
 {"id": "missing-system", "code": {"coding": [{"display": "No system"}]}}