Improve defining and loading clinical codes/codelists

opensafely · Dec 6, 2024 · 3e7056e · 3e7056e
1 parent d23e050
commit 3e7056e
Show file tree

Hide file tree

Showing 5 changed files with 20 additions and 32 deletions.
diff --git a/analysis/codelists.py b/analysis/codelists.py
@@ -68,3 +68,16 @@
 # Community Pharmacist Consultation Service for minor illness - 1577041000000109
 # Pharmacy First service - 983341000000102
 pharmacy_first_consultation_codelist = ["1577041000000109", "983341000000102"]
+
+# PF codes separated for individual analysis
+pharmacy_first_event_codes = {
+    # # Community Pharmacy (CP) Blood Pressure (BP) Check Service (procedure)
+    # "blood_pressure_service": ["1659111000000107"],
+    # # Community Pharmacy (CP) Contraception Service (procedure)
+    # "contraception_service": ["1659121000000101"],
+    # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
+    "consultation_service": ["1577041000000109"],
+    # Pharmacy First service (qualifier value)
+    "pharmacy_first_service": ["983341000000102"],
+    "combined_pf_service": ["1577041000000109", "983341000000102"],
+}
diff --git a/analysis/measures_definition_pf_breakdown.py b/analysis/measures_definition_pf_breakdown.py
@@ -11,7 +11,8 @@
     ethnicity_codelist,
 )
 
-from pf_dataset import pharmacy_first_event_codes, get_latest_ethnicity
+from pf_dataset import get_latest_ethnicity
+from codelists import pharmacy_first_event_codes, pharmacy_first_consultation_codelist
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -58,7 +59,7 @@
 
 pharmacy_first_ids = clinical_events.where(
     clinical_events.snomedct_code.is_in(
-        pharmacy_first_event_codes["combined_pf_service"]
+        pharmacy_first_consultation_codelist
     )
 ).consultation_id
 

diff --git a/analysis/measures_definition_pf_condition_provider.py b/analysis/measures_definition_pf_condition_provider.py
@@ -8,8 +8,7 @@
     pharmacy_first_conditions_codes,
     imd_quintile,
 )
-from pf_dataset import pharmacy_first_event_codes
-
+from codelists import pharmacy_first_consultation_codelist
 
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
@@ -26,7 +25,7 @@
 # Create variable which contains boolean values of whether pharmacy first event exists for patient
 has_pharmacy_first = selected_events.where(
     selected_events.snomedct_code.is_in(
-        pharmacy_first_event_codes["combined_pf_service"]
+        pharmacy_first_consultation_codelist
     )
 ).exists_for_patient()
 

diff --git a/analysis/measures_definition_pf_medications.py b/analysis/measures_definition_pf_medications.py
@@ -5,20 +5,8 @@
     practice_registrations,
 )
 from ehrql.tables.raw.tpp import medications
-
-from pf_dataset import pharmacy_first_event_codes
 from codelists import *
 
-pharmacy_first_med_codes = (
-    acute_otitis_media_tx_cod
-    + impetigo_treatment_tx_cod
-    + infected_insect_bites_tx_cod
-    + shingles_treatment_tx_cod
-    + sinusitis_tx_cod
-    + sore_throat_tx_cod
-    + urinary_tract_infection_tx_cod
-)
-
 measures = create_measures()
 measures.configure_dummy_data(population_size=1000)
 # Turn off during code development, but turn on before running against on the server
@@ -34,7 +22,7 @@
     clinical_events.date.is_on_or_between(INTERVAL.start_date, INTERVAL.end_date)
 ).where(
     clinical_events.snomedct_code.is_in(
-        pharmacy_first_event_codes["combined_pf_service"]
+        pharmacy_first_consultation_codelist
     )
 )
 
@@ -53,7 +41,7 @@
 
 # Check if a medication is from our PF codelists 
 has_pharmacy_first_medication = first_selected_medication.is_in(
-    pharmacy_first_med_codes
+    pharmacy_first_med_codelist
 )
 
 # Numerator, patients with a PF medication

diff --git a/analysis/pf_dataset.py b/analysis/pf_dataset.py
@@ -2,19 +2,6 @@
 
 from pf_variables_library import check_pregnancy_status, count_past_events
 
-pharmacy_first_event_codes = {
-    # # Community Pharmacy (CP) Blood Pressure (BP) Check Service (procedure)
-    # "blood_pressure_service": ["1659111000000107"],
-    # # Community Pharmacy (CP) Contraception Service (procedure)
-    # "contraception_service": ["1659121000000101"],
-    # Community Pharmacist (CP) Consultation Service for minor illness (procedure)
-    "consultation_service": ["1577041000000109"],
-    # Pharmacy First service (qualifier value)
-    "pharmacy_first_service": ["983341000000102"],
-    "combined_pf_service": ["1577041000000109", "983341000000102"],
-}
-
-
 # Create denominator variables for each clinical condition
 # These are based on NHS England rules using sex, age, pregnancy status and repeated diagnoses
 # NOTE: The following exclusions have not been added: