new repo with more flexible code

analysis/codelists.py

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+# import ehrql function for importing codelists
+from ehrql import (
+  codelist_from_csv
+)
+
+# ethnicity codes
+ethnicity_codes = codelist_from_csv(
+    "codelists/opensafely-ethnicity-snomed-0removed.csv",
+    column = "snomedcode",
+    category_column = "Grouping_6",
+)
+ethnicity_codes_16 = codelist_from_csv(
+    "codelists/opensafely-ethnicity-snomed-0removed.csv",
+    column = "snomedcode",
+    category_column = "Grouping_16",
+)
+
+# smoking
+clear_smoking_codes = codelist_from_csv(
+    "codelists/opensafely-smoking-clear.csv",
+    column = "CTV3Code",
+    category_column = "Category",
+)
+
+unclear_smoking_codes = codelist_from_csv(
+    "codelists/opensafely-smoking-unclear.csv",
+    column = "CTV3Code",
+    category_column = "Category",
+)
+
+# drinking
+drinking_codelist = codelist_from_csv(
+  "codelists/user-angel-wong-hazardous-drinking.csv",
+  column = "code",
+)
+
+# illicit substances 
+drug_usage_codelist = codelist_from_csv(
+  "codelists/nhsd-primary-care-domain-refsets-illsub_cod.csv",
+  column = "code",
+)
+drug_intervention_codelist = codelist_from_csv(
+  "codelists/nhsd-primary-care-domain-refsets-illsubint_cod.csv",
+  column = "code",
+)
+drug_assessment_declination_codelist = codelist_from_csv(
+  "codelists/nhsd-primary-care-domain-refsets-illsubassdec_cod.csv",
+  column = "code",
+)
+
+# asthma diagnosis
+asthma_codelist = codelist_from_csv(
+    "codelists/nhsd-primary-care-domain-refsets-ast_cod.csv",
+    column = "code",
+)
+
+# asthma medications
+asthma_medications = codelist_from_csv(
+  "codelists/opensafely-asthma-inhaler-steroid-medication.csv",
+  column = "code",
+)
+
+# reactive airway disease code
+reactive_airway_disease_code = ["266898002"]
+
+# COPD
+copd_codelist = codelist_from_csv(
+  "codelists/nhsd-primary-care-domain-refsets-copd_cod.csv",
+  column = "code",
+)
+copd_medications = codelist_from_csv(
+  "codelists/bristol-copd-medications-bnf.csv",
+  column = "code",
+)
+
+# pulmonary fibrosis
+pulmonary_fibrosis_codelist = codelist_from_csv(
+  "codelists/bristol-ild-snomed.csv",
+  column = "code",
+)
+
+# # hypertension
+# hypertension_codelist = codelist_from_csv(
+#   "codelists/nhsd-primary-care-domain-refsets-hyp_cod.csv",
+#   column = "code",
+# )
+# 
+# # type 1 diabetes
+# type1_diabetes_codelist = codelist_from_csv(
+#   "codelists/nhsd-primary-care-domain-refsets-dmtype1_cod.csv",
+#   column = "code",
+# )
+# 
+# # non-type 1 diabetes
+# non_type1_diabetes_codelist = codelist_from_csv(
+#   "codelists/nhsd-primary-care-domain-refsets-dmnontype1_cod.csv",
+#   column = "code",
+# )
+# 
+# # heart failure
+# heart_failure_codelist = codelist_from_csv(
+#   "codelists/nhsd-primary-care-domain-refsets-hf_cod.csv",
+#   column = "code",
+# )
+# 
+# # prior MI
+# prior_mi_codelist = codelist_from_csv(
+#   "codelists/nhsd-primary-care-domain-refsets-mi_cod.csv",
+#   column = "code",
+# )
+
+# rsv primary - specific 
+
+# rsv secondary - specific
+
+# covid primary - specific
+covid_primary_codelist = codelist_from_csv(
+  "codelists/opensafely-covid-identification-in-primary-care-probable-covid-positive-test.csv",
+  column = "CTV3ID",
+)
+
+# covid secondary - specific
+covid_secondary_codelist = codelist_from_csv(
+  "codelists/opensafely-covid-identification.csv",
+  column = "icd10_code",
+)
+
+# flu primary - specific
+
+# flu secondary - specific
+
+# rsv primary - sensitive 
+
+# rsv secondary - sensitive
+
+# covid primary - sensitive
+covid_primary_codelist = codelist_from_csv(
+  "codelists/opensafely-covid-identification-in-primary-care-probable-covid-positive-test.csv",
+  column = "CTV3ID",
+)
+
+# covid secondary - sensitive
+covid_secondary_codelist = codelist_from_csv(
+  "codelists/opensafely-covid-identification.csv",
+  column = "icd10_code",
+)
+
+# flu primary - sensitive
+
+# flu secondary - sensitive
+
+##exclusion criteria
+
+# care home 
+care_home_codelist = codelist_from_csv(
+  "codelists/nhsd-primary-care-domain-refsets-carehome_cod.csv",
+  column = "code",
+)
+
+# severe combined immunodeficiency syndrome
+severe_immunodeficiency_code = ["31323000"]
+
+# requiring ventilation
+ventilation_codes = ["Z99.1", "P28.8"]
+
+# cardiac disease
+cardiac_disease_codelist = codelist_from_csv(
+  "codelists/opensafely-chronic-cardiac-disease.csv",
+  column = "CTV3ID",
+)
+
+# pulmonary hypertension
+pulmonary_hypertension_codelist = codelist_from_csv(
+  "codelists/nhsd-primary-care-domain-refsets-pulmohyp_cod.csv",
+  column = "code", 
+)