Run ruff format

opensafely · Jan 29, 2025 · a9e9b5e · a9e9b5e
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Showing 8 changed files with 159 additions and 159 deletions.
diff --git a/analysis/codelists.py b/analysis/codelists.py
@@ -87,7 +87,8 @@
     # Community Pharmacy Pharmacy First Service
     "pf_consultation_cp_service": pf_consultation_cp_service,
     "pf_consultation_services_combined": pf_consultation_cp_minorillness
-    + pf_consultation_service + pf_consultation_cp_service,
+    + pf_consultation_service
+    + pf_consultation_cp_service,
 }
 
 uti_code = ["1090711000000102"]
@@ -96,4 +97,4 @@
 otitismedia_code = ["3110003"]
 sorethroat_code = ["363746003"]
 shingles_code = ["4740000"]
-impetigo_code = ["48277006"]
+impetigo_code = ["48277006"]
diff --git a/analysis/dataset_definition_table1.py b/analysis/dataset_definition_table1.py
@@ -18,7 +18,7 @@
     get_numerator,
     get_latest_ethnicity,
     get_age_band,
-    get_imd
+    get_imd,
 )
 from pf_variables_library import select_events
 import codelists
@@ -27,15 +27,21 @@
 dataset = create_dataset()
 
 registration = practice_registrations.for_patient_on(index_date)
-selected_events = clinical_events.where(clinical_events.date.is_on_or_before(index_date))
+selected_events = clinical_events.where(
+    clinical_events.date.is_on_or_before(index_date)
+)
 
 # Columns for demographics table
 dataset.sex = patients.sex
 dataset.age_band = get_age_band(patients, index_date)
 dataset.region = registration.practice_nuts1_region_name
 dataset.imd = get_imd(addresses, index_date)
 dataset.ethnicity = get_latest_ethnicity(
-    index_date, selected_events, codelists.ethnicity_group16_codelist, ethnicity_from_sus, grouping=16
+    index_date,
+    selected_events,
+    codelists.ethnicity_group16_codelist,
+    ethnicity_from_sus,
+    grouping=16,
 )
 
 
@@ -65,17 +71,36 @@
     index_date, selected_events, codelists.pregnancy_codelist
 )
 
-dataset.uti_numerator = get_numerator(selected_events, codelists.uti_code, dataset.uti_denominator)
-dataset.sinusitis_numerator = get_numerator(selected_events, codelists.sinusitis_code, dataset.sinusitis_denominator)
-dataset.insectbite_numerator = get_numerator(selected_events, codelists.insectbite_code, dataset.insectbite_denominator)
-dataset.otitismedia_numerator = get_numerator(selected_events, codelists.otitismedia_code, dataset.otitismedia_denominator)
-dataset.sorethroat_numerator = get_numerator(selected_events, codelists.sorethroat_code, dataset.sorethroat_denominator)
-dataset.shingles_numerator = get_numerator(selected_events, codelists.shingles_code, dataset.shingles_denominator)
-dataset.impetigo_numerator = get_numerator(selected_events, codelists.impetigo_code, dataset.impetigo_denominator)
+dataset.uti_numerator = get_numerator(
+    selected_events, codelists.uti_code, dataset.uti_denominator
+)
+dataset.sinusitis_numerator = get_numerator(
+    selected_events, codelists.sinusitis_code, dataset.sinusitis_denominator
+)
+dataset.insectbite_numerator = get_numerator(
+    selected_events, codelists.insectbite_code, dataset.insectbite_denominator
+)
+dataset.otitismedia_numerator = get_numerator(
+    selected_events, codelists.otitismedia_code, dataset.otitismedia_denominator
+)
+dataset.sorethroat_numerator = get_numerator(
+    selected_events, codelists.sorethroat_code, dataset.sorethroat_denominator
+)
+dataset.shingles_numerator = get_numerator(
+    selected_events, codelists.shingles_code, dataset.shingles_denominator
+)
+dataset.impetigo_numerator = get_numerator(
+    selected_events, codelists.impetigo_code, dataset.impetigo_denominator
+)
 
-pf_consultation_events = select_events(selected_events, codelist=codelists.pf_consultation_events_dict["pf_consultation_services_combined"])
+pf_consultation_events = select_events(
+    selected_events,
+    codelist=codelists.pf_consultation_events_dict["pf_consultation_services_combined"],
+)
 has_pf_consultation = pf_consultation_events.exists_for_patient()
 
 dataset.define_population(
-    registration.exists_for_patient() & patients.sex.is_in(["male", "female"]) & has_pf_consultation
+    registration.exists_for_patient()
+    & patients.sex.is_in(["male", "female"])
+    & has_pf_consultation
 )
diff --git a/analysis/measures_definition_pf_breakdown.py b/analysis/measures_definition_pf_breakdown.py
@@ -13,7 +13,10 @@
 
 from pf_dataset import get_latest_ethnicity
 from codelists import pf_consultation_events_dict
-from config import start_date_measure_pf_breakdown, monthly_intervals_measure_pf_breakdown
+from config import (
+    start_date_measure_pf_breakdown,
+    monthly_intervals_measure_pf_breakdown,
+)
 from pf_variables_library import select_events
 
 measures = create_measures()
@@ -59,12 +62,15 @@
     otherwise="Missing",
 )
 
-pharmacy_first_ids = select_events(clinical_events, codelist=pf_consultation_events_dict["pf_consultation_services_combined"]).consultation_id
+pharmacy_first_ids = select_events(
+    clinical_events,
+    codelist=pf_consultation_events_dict["pf_consultation_services_combined"],
+).consultation_id
 
 # # Select clinical events in interval date range
-selected_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date).where(
-    clinical_events.consultation_id.is_in(pharmacy_first_ids)
-)
+selected_events = select_events(
+    clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
+).where(clinical_events.consultation_id.is_in(pharmacy_first_ids))
 
 # Breakdown metrics to be produced as graphs
 breakdown_metrics = {
@@ -75,11 +81,18 @@
     "ethnicity": ethnicity_combined,
 }
 
-pf_consultation_events = select_events(selected_events, codelist=pf_consultation_events_dict["pf_consultation_services_combined"])
+pf_consultation_events = select_events(
+    selected_events,
+    codelist=pf_consultation_events_dict["pf_consultation_services_combined"],
+)
 has_pf_consultation = pf_consultation_events.exists_for_patient()
 
 # Define the denominator as the number of patients registered
-denominator = registration.exists_for_patient() & patients.sex.is_in(["male", "female"]) & has_pf_consultation
+denominator = (
+    registration.exists_for_patient()
+    & patients.sex.is_in(["male", "female"])
+    & has_pf_consultation
+)
 
 # Create measures for pharmacy first services
 for pharmacy_first_event, codelist in pf_consultation_events_dict.items():
@@ -150,4 +163,4 @@
             denominator=pf_condition_denominators[condition_name],
             group_by={breakdown: variable},
             intervals=months(monthly_intervals).starting_on(start_date),
-        )
+        )
diff --git a/analysis/measures_definition_pf_condition_provider.py b/analysis/measures_definition_pf_condition_provider.py
@@ -9,7 +9,10 @@
     imd_quintile,
 )
 from codelists import pf_consultation_events_dict
-from config import start_date_measure_condition_provider, monthly_intervals_measure_condition_provider
+from config import (
+    start_date_measure_condition_provider,
+    monthly_intervals_measure_condition_provider,
+)
 from pf_variables_library import select_events
 
 measures = create_measures()
@@ -20,10 +23,15 @@
 
 registration = practice_registrations.for_patient_on(INTERVAL.end_date)
 
-selected_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date)
+selected_events = select_events(
+    clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
+)
 
 # Create variable which contains boolean values of whether pharmacy first event exists for patient
-has_pharmacy_first = select_events(selected_events, codelist=pf_consultation_events_dict["pf_consultation_services_combined"]).exists_for_patient()
+has_pharmacy_first = select_events(
+    selected_events,
+    codelist=pf_consultation_events_dict["pf_consultation_services_combined"],
+).exists_for_patient()
 
 for condition_name, condition_code in pharmacy_first_conditions_codes.items():
     condition_events = selected_events.where(
@@ -32,16 +40,15 @@
 
     # Define the numerator as the count of events for the condition
     numerator = condition_events.count_for_patient()
-    denominator = registration.exists_for_patient() & patients.sex.is_in(["male", "female"])
+    denominator = registration.exists_for_patient() & patients.sex.is_in(
+        ["male", "female"]
+    )
 
     # Measures for overall clinical services graph
     measures.define_measure(
         name=f"count_{condition_name}_total",
         numerator=numerator,
         denominator=denominator,
-        group_by={
-            "pf_status": has_pharmacy_first,
-            "imd": imd_quintile
-        },
+        group_by={"pf_status": has_pharmacy_first, "imd": imd_quintile},
         intervals=months(monthly_intervals).starting_on(start_date),
-    )
+    )
diff --git a/analysis/measures_definition_pf_consultation_med_counts.py b/analysis/measures_definition_pf_consultation_med_counts.py
@@ -25,21 +25,19 @@
 
 # Select Pharmacy First events during interval date range
 pharmacy_first_events = select_events(
-    clinical_events, 
-    start_date=INTERVAL.start_date, 
-    end_date=INTERVAL.end_date).where(
-        clinical_events.snomedct_code.is_in(
-            pf_consultation_events_dict["pf_consultation_services_combined"]
-        )
+    clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
+).where(
+    clinical_events.snomedct_code.is_in(
+        pf_consultation_events_dict["pf_consultation_services_combined"]
     )
+)
 
 pharmacy_first_ids = pharmacy_first_events.consultation_id
 has_pf_consultation = pharmacy_first_events.exists_for_patient()
 
 # Select Pharmacy First consultations during interval date range
 selected_medications = select_events(
-    medications,
-    start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
+    medications, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
 ).where(medications.consultation_id.is_in(pharmacy_first_ids))
 
 # First medication for each patient
@@ -62,7 +60,7 @@
 
 measures.define_measure(
     name="pf_medication_count",
-    numerator = first_selected_medication.is_not_null(),
+    numerator=first_selected_medication.is_not_null(),
     denominator=denominator,
     group_by={
         "dmd_code": first_selected_medication,

diff --git a/analysis/measures_definition_pf_medications.py b/analysis/measures_definition_pf_medications.py
@@ -20,27 +20,29 @@
 registration = practice_registrations.for_patient_on(INTERVAL.end_date)
 
 # Select Pharmacy First consultations during interval date range
-pharmacy_first_events = select_events(clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date).where(
-    clinical_events.snomedct_code.is_in(pf_consultation_events_dict["pf_consultation_services_combined"])
+pharmacy_first_events = select_events(
+    clinical_events, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
+).where(
+    clinical_events.snomedct_code.is_in(
+        pf_consultation_events_dict["pf_consultation_services_combined"]
+    )
 )
 
 pharmacy_first_ids = pharmacy_first_events.consultation_id
 has_pf_consultation = pharmacy_first_events.exists_for_patient()
 
 # Select medications prescribed with PF consultation ID
-selected_medications = select_events(medications, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date).where(
-    medications.consultation_id.is_in(pharmacy_first_ids)
-)
+selected_medications = select_events(
+    medications, start_date=INTERVAL.start_date, end_date=INTERVAL.end_date
+).where(medications.consultation_id.is_in(pharmacy_first_ids))
 
 # Select first medication for group_by argument in measures
 first_selected_medication = (
     selected_medications.sort_by(medications.date).first_for_patient().dmd_code
 )
 
-# Check if a medication is from our PF codelists 
-has_pharmacy_first_medication = first_selected_medication.is_in(
-    pf_med_codelist
-)
+# Check if a medication is from our PF codelists
+has_pharmacy_first_medication = first_selected_medication.is_in(pf_med_codelist)
 
 # Numerator, patients with a PF medication
 # This allows me to count all (first) medications linked to a PF consultation
@@ -58,8 +60,6 @@
     name="pf_medication_count",
     numerator=has_pharmacy_first_medication,
     denominator=denominator,
-    group_by={
-        "dmd_code": first_selected_medication
-    },
+    group_by={"dmd_code": first_selected_medication},
     intervals=months(monthly_intervals).starting_on(start_date),
 )