chore: Update external_studies test code

tests/acceptance/external_studies/mainroute_cancer/analysis/codelists.py

@@ -55,3 +55,7 @@
     column="snomedcode",
     category_column="Grouping_6",
 )
+
+lowerGI_diagnostic_codes = codelist_from_csv(
+    "local_codelists/phc-lowergi-endoscopy-hrg.csv", column="code"
+)

tests/acceptance/external_studies/mainroute_cancer/analysis/define_static_dataset.py

@@ -1,7 +1,8 @@
 from ehrql import case, when, years, days, minimum_of, maximum_of
-from ehrql.tables.core import patients, clinical_events
+from ehrql.tables.core import patients
 from ehrql.tables.tpp import ( 
     addresses,
+    clinical_events,
     practice_registrations)
 
 import codelists
@@ -29,6 +30,13 @@
             clinical_events.date.is_on_or_between(index_date, end_date)
         ).exists_for_patient()
 
+dataset.colorectal_ca_diag_date = clinical_events.where(clinical_events.snomedct_code.is_in(codelists.colorectal_diagnosis_codes_snomed)
+        ).where(
+            clinical_events.date.is_on_or_between(index_date, end_date)
+        ).sort_by(
+            clinical_events.date
+        ).first_for_patient().date
+
 age = patients.age_on(dataset.entry_date)
 dataset.age = age
 dataset.age_group = case(
@@ -74,3 +82,29 @@
 )
 
 dataset.region = practice_registrations.for_patient_on(dataset.entry_date).practice_nuts1_region_name
+
+def num_event(codelist, l_age, u_age):
+    return clinical_events.where(clinical_events.snomedct_code.is_in(codelist)
+        ).where(
+            clinical_events.date.is_on_or_between(index_date, end_date)
+        ).where(
+            clinical_events.date.is_on_or_between(dataset.entry_date, dataset.exit_date)
+        ).where(
+            patients.age_on(clinical_events.date)>=l_age
+        ).where(
+            patients.age_on(clinical_events.date)<u_age
+        ).date.count_episodes_for_patient(days(42))
+
+dataset.num_ida = num_event(codelists.ida_codes, 16, 111)
+dataset.num_cibh = num_event(codelists.cibh_codes, 16, 111)
+dataset.num_prbleed = num_event(codelists.prbleeding_codes, 16, 111)
+dataset.num_wl = num_event(codelists.wl_codes, 16, 111)
+dataset.num_abdomass = num_event(codelists.abdomass_codes, 16, 111)
+dataset.num_abdopain = num_event(codelists.abdopain_codes, 16, 111)
+dataset.num_anaemia = num_event(codelists.anaemia_codes, 16, 111)
+dataset.num_prbleed_50 = num_event(codelists.prbleeding_codes, 50, 111)
+dataset.num_wl_50 = num_event(codelists.wl_codes, 50, 111)
+dataset.num_abdopain_50 = num_event(codelists.abdopain_codes, 50, 111)
+dataset.num_anaemia_60 = num_event(codelists.anaemia_codes, 60, 111)
+
+dataset.num_lowerGI_any_symp = num_event(codelists.colorectal_symptom_codes, 16, 111)

tests/acceptance/external_studies/mainroute_cancer/analysis/measures_demo.py

@@ -64,12 +64,12 @@
 
 measures.define_defaults(intervals=months(intervals).starting_on(start_date))
 
-measures.define_measure(
-    name="fit_test_rate", 
-    numerator=dataset.fit_test_any,
-    denominator=dataset.elig_cohort,
-    group_by={"imd": imd5}
-    )
+#measures.define_measure(
+    #name="fit_test_rate", 
+    #numerator=dataset.fit_test_any,
+    #denominator=dataset.elig_cohort,
+    #group_by={"imd": imd5}
+    #)
 
 measures.define_measure(
     name="ida_symp_rate", 
@@ -120,16 +120,16 @@
     group_by={"imd": imd5}
     )
 
-measures.define_measure(
-    name="fit_6_rate", 
-    numerator=dataset.fit_6_all_lowerGI,
-    denominator=dataset.elig_cohort,
-    group_by={"imd": imd5}
-    )
-
-measures.define_measure(
-    name="ca_6_rate", 
-    numerator=dataset.ca_6_all_lowerGI,
-    denominator=dataset.lowerGI_any_symp,
-    group_by={"imd": imd5}
-    )
+#measures.define_measure(
+    #name="fit_6_rate", 
+    #numerator=dataset.fit_6_all_lowerGI,
+    #denominator=dataset.elig_cohort,
+    #group_by={"imd": imd5}
+    #)
+
+#measures.define_measure(
+    #name="ca_6_rate", 
+    #numerator=dataset.ca_6_all_lowerGI,
+    #denominator=dataset.lowerGI_any_symp,
+    #group_by={"imd": imd5}
+    #)

tests/acceptance/external_studies/waiting-list/analysis/codelists.py

@@ -16,36 +16,32 @@
     column = "code"
 )
 
-# lo_opioid_codes = codelist_from_csv(
-#     "codelists/opensafely-long-acting-opioids-less-than-50mg-per-day-ome-dmd.csv",
-#     column = "code"
-# )
-
-# med_opioid_codes = codelist_from_csv(
-#     "codelists/opensafely-long-acting-opioids-50mg-to-119mg-per-day-ome-dmd.csv",
-#     column = "code"
-# )
-
-# hi_opioid_codes = codelist_from_csv(
-#     "codelists/opensafely-long-acting-opioids-greater-than-or-equal-to-120mg-per-day-ome-dmd.csv",
-#     column = "code"
-# )
-
 long_opioid_codes = codelist_from_csv(
     "codelists/user-anschaf-long-acting-opioids-dmd.csv",
     column = "code"
 )
 
-strong_opioid_codes = codelist_from_csv(
+strong_opioid_codes1 = codelist_from_csv(
     "codelists/opensafely-strongopioidsCW-dmd.csv",
     column = "code"
 )
 
+strong_opioid_codes2 = codelist_from_csv(
+    "codelists/user-anschaf-strong-opioids-exc-tramadol-and-tapentadol-dmd.csv",
+    column = "code"
+)
+
 weak_opioid_codes = codelist_from_csv(
     "codelists/user-anschaf-weak-opioids-dmd.csv",
     column = "code"
 )
 
+moderate_opioid_codes = codelist_from_csv(
+    "codelists/user-anschaf-tramadol-and-tapentadol-dmd.csv",
+    column = "code"
+)
+
+
 short_opioid_codes = set(opioid_codes) - set(long_opioid_codes)
 
 
@@ -109,8 +105,8 @@
 )
 
 osteoarthritis_codes = codelist_from_csv(
-    "codelists/opensafely-osteoarthritis.csv",
-    column = "CTV3ID"
+    "codelists/user-speed-vm-osteoarthritis-snomed-ct.csv",
+    column = "code"
 )
 
 depression_codes = codelist_from_csv(
@@ -129,41 +125,65 @@
 )
 
 cardiac_codes = codelist_from_csv(
-  "codelists/opensafely-chronic-cardiac-disease.csv",
-  column = "CTV3ID"
+  "codelists/primis-covid19-vacc-uptake-chd_cov.csv",
+  column = "code"
 )
 
 ckd_codes = codelist_from_csv(
-  "codelists/opensafely-chronic-kidney-disease-snomed.csv",
-  column = "id"
+  "codelists/primis-covid19-vacc-uptake-ckd15.csv",
+  column = "code"
 )
 
 liver_codes = codelist_from_csv(
-  "codelists/opensafely-chronic-liver-disease.csv",
-  column = "CTV3ID"
+  "codelists/primis-covid19-vacc-uptake-cld.csv",
+  column = "code"
 )
 
 diabetes_codes = codelist_from_csv(
-  "codelists/opensafely-diabetes.csv",
-  column = "CTV3ID"
+  "codelists/primis-covid19-vacc-uptake-diab.csv",
+  column = "code"
 )
 
 copd_codes = codelist_from_csv(
-  "codelists/opensafely-chronic-respiratory-disease.csv",
-  column = "CTV3ID"
+  "codelists/primis-covid19-vacc-uptake-resp_cov.csv",
+  column = "code"
 )
 
 ra_codes = codelist_from_csv(
-  "codelists/opensafely-rheumatoid-arthritis.csv",
-  column = "CTV3ID"
+  "codelists/user-markdrussell-new-rheumatoid-arthritis.csv",
+  column = "code"
 )
 
 oud_codes = codelist_from_csv(
   "codelists/user-hjforbes-opioid-dependency-clinical-diagnosis.csv",
   column = "code"
 )
 
-pain_codes = codelist_from_csv(
-  "codelists/opensafely-symptoms-pain.csv",
-  column = "code"
-)
+### HRG codes
+hip_codes = ["HN12A","HN12B","HN12C","HN12D","HN12E","HN12F","HN13A","HN13B","HN13C","HN13D","HN13E","HN13F","HN13G","HN13H",
+              "HN14A","HN14B","HN14C","HN14D","HN14E","HN14F","HN14G","HN14H","HN15A","HN15B","HN16A","HN16B","HN16C"]
+
+knee_codes = ["HN22A","HN22B","HN22C","HN22D","HN22E","HN23A","HN23B","HN23C","HN23D","HN23E",
+              "HN24A","HN24B","HN24C","HN24D","HN24E","HN24F","HN25A","HN25B","HN26A","HN26B","HN26C"]
+
+foot_codes = ["HN32A","HN32B","HN32C","HN33A","HN33B","HN33C","HN33D","HN34A","HN34B","HN34C","HN34D","HN35A","HN35B","HN36Z"]
+
+hand_codes = ["HN42A","HN42B","HN43A","HN43B","HN43C","HN44A","HN44B","HN44C","HN44D","HN45A","HN45B","HN45C","HN46Z"]
+
+shoulder_codes = ["HN52A","HN52B","HN52C","HN53A","HN53B","HN53C",
+                 "HN54A","HN54B","HN54C","HN54D","HN55Z","HN56Z"]
+
+elbow_codes = ["HN62A","HN62B","HN63A","HN63B","HN64A","HN64B","HN64C","HN64D","HN65Z","HN66Z"]
+
+complex_codes = ["HN80A","HN80B","HN80C","HN80D","HN81A","HN81B","HN81C","HN81D","HN81E","HN85Z","HN86A","HN86B","HN93Z"]
+
+pain_codes = ["AB11Z","AB12Z","AB13Z","AB14Z","AB15Z","AB16Z","AB17Z","AB18Z","AB19Z","AB20Z",
+            "AB21Z","AB22Z","AB23Z","AB24Z","AB25Z","AB26Z","AB27Z","AB28Z"]
+
+trauma_codes = ["HT12A","HT12B","HT12C","HT12D","HT12E","HT13A","HT13B","HT13C","HT13D","HT13E",
+                "HT14A","HT14B","HT14C","HT15Z","HT22A","HT22B","HT22C","HT23A","HT23B","HT23C","HT23D","HT23E",
+                "HT24A","HT24B","HT24C","HT24D","HT25Z","HT32A","HT32B","HT32C","HT33A","HT33B","HT33C","HT33D","HT33E",
+                "HT34A","HT34B","HT34C","HT34D","HT34E","HT35Z","HT42A","HT42B","HT43A","HT43B","HT43C","HT43D","HT43E",
+                "HT44A","HT44B","HT44C","HT44D","HT44E","HT45Z","HT52A","HT52B","HT52C","HT53A","HT53B","HT53C","HT53D","HT53E",
+                "HT54A","HT54B","HT54C","HT54D","HT55Z","HT62A","HT62B","HT63A","HT63B","HT63C","HT63D","HT63E","HT63F",
+                "HT64A","HT64B","HT64C","HT64D","HT65Z","HT81A","HT81B","HT81C","HT81D","HT86A","HT86B","HT86C"]