Merge pull request #976 from opensafely-core/steve/remove-ons-cis

Remove ONS CIS data

cohortextractor/patients.py

@@ -2842,90 +2842,6 @@ def with_an_isaric_record(
  return "with_an_isaric_record", locals()
 
 
-def with_an_ons_cis_record(
- returning,
- return_category_labels=True,
- # Date filtering: column to filter
- date_filter_column=None,
- # Date filtering: date limits
- on_or_before=None,
- on_or_after=None,
- between=None,
- # Matching rule
- find_first_match_in_period=None,
- find_last_match_in_period=None,
- include_date_of_match=False,
- date_format=None,
- return_expectations=None,
-):
- """
- Return whether patient has an ONS CIS record
-
- Args:
- returning: string value; options are:
-
- * "binary_flag"
- * "number_of_matches_in_period"
- * the ONS CIS table column to return
- return_category_labels: If the value of `returning` is a coded category, return the
- the corresponding longform string labels
- date_filter_column: the ONS CIS column to use with date limit args; options are:
-
- * "covid_date"
- * "covid_test_blood_neg_last_date"
- * "covid_test_blood_pos_first_date"
- * "covid_test_swab_neg_last_date"
- * "covid_test_swab_pos_first_date"
- * "received_ox_date"
- * "result_mk_date"
- * "samples_taken_date"
- * "sympt_now_date"
- * "travel_abroad_date"
- * "visit_date"
-
- `date_filter_column` is not required when returning "number_of_matches_in_period", with no
- date limit arguments. It is required for all other `returning` options
-
- on_or_before: date of interest as a string with the format `YYYY-MM-DD`. Filters results to measurements
- on or before the given date (as defined by `date_filter_column`).
- on_or_after: date of interest as a string with the format `YYYY-MM-DD`. Filters results to measurements
- on or after the given date (as defined by `date_filter_column`).
- between: two dates of interest as a list with each date as a string with the format `YYYY-MM-DD`.
- Filters results to measurements between the two dates (as defined by `date_filter_column`)
- provided (inclusive).
- The two dates must be in chronological order.
- find_first_match_in_period: as described elsewhere
- find_last_match_in_period: as described elsewhere
- include_date_of_match: a boolean indicating if an extra column containing the date (from `date_filter_column`)
- of the match should be returned.
- date_format: a string detailing the format of dates to be returned.
- It can be "YYYY-MM-DD", "YYYY-MM" or "YYYY" and wherever possible the least disclosive data should be
- returned. i.e returning only year is less disclosive than a date with month and year.
- return_expectations: as described elsewhere.
-
- Example:
- Return cleaned employment status (as longform category labels) for patients with a positive covid blood test
- after 01 Jan 2022, returning also the date of the positive covid blood test:
-
- employment_status = patients.with_an_ons_cis_record(
- returning="work_status_clean",
- return_category_labels=True,
- date_filter_column="covid_test_blood_pos_first_date",
- on_or_after="2022-01-01",
- find_first_match_in_period=True,
- include_date_of_match=True,
- date_format="YYYY-MM-DD",
- return_expectations={
- "rate": "universal",
- "category": {
- "ratios": {"Not working": 0.2, "Working": 0.6, "Student": 0.2},
- },
- },
- )
- """
- return "with_an_ons_cis_record", locals()
-
-
 def with_record_in_ukrr(
  # picks dataset held by UK Renal Registry (UKRR)
  from_dataset=None,

cohortextractor/process_covariate_definitions.py

@@ -2,8 +2,6 @@
 import datetime
 import re
 
-from .ons_cis_utils import ONS_CIS_CATEGORY_COLUMNS, ONS_CIS_COLUMN_MAPPINGS
-
 # ISARIC data has a lot of columns that are all varchar in the db.
 ISARIC_COLUMN_MAPPINGS = {
  "abdopain_ceoccur_v2": "str",
@@ -813,13 +811,6 @@ def type_of_with_covid_therapeutics(self, returning, **kwargs):
  def type_of_with_an_isaric_record(self, returning, **kwargs):
  return ISARIC_COLUMN_MAPPINGS[returning]
 
- def type_of_with_an_ons_cis_record(self, returning, **kwargs):
- if returning in ONS_CIS_CATEGORY_COLUMNS:
- return "str"
- elif returning in ONS_CIS_COLUMN_MAPPINGS:
- return ONS_CIS_COLUMN_MAPPINGS[returning]
- return self._type_from_return_value(returning)
-
  def type_of_with_record_in_ukrr(self, returning, **kwargs):
  return self._type_from_return_value(returning)