From cc204eb4d10acbd1da994b1acaf2a9f580d82741 Mon Sep 17 00:00:00 2001
From: Peter Inglesby <peter.inglesby@gmail.com>
Date: Tue, 7 Nov 2023 10:27:46 +0000
Subject: [PATCH] Replace cohortextractor with ehrql

Fixes #108
---
 analysis/dataset_definition.py |  5 -----
 analysis/study_definition.py   | 17 -----------------
 project.yaml                   | 14 ++++----------
 3 files changed, 4 insertions(+), 32 deletions(-)
 delete mode 100644 analysis/study_definition.py

diff --git a/analysis/dataset_definition.py b/analysis/dataset_definition.py
index 6202e23..8ca2273 100644
--- a/analysis/dataset_definition.py
+++ b/analysis/dataset_definition.py
@@ -1,8 +1,3 @@
-# Note: If you are using ehrQL to define your study population you need to:
-# (1) uncomment the ehrQL action in the project.yaml file (lines 14-18),
-# (2) delete the cohort-extractor action from the project.yaml file (lines 8-12), and
-# (3) delete the study_definition.py file.
-
 from ehrql import Dataset
 from ehrql.tables.beta.tpp import patients, practice_registrations
 
diff --git a/analysis/study_definition.py b/analysis/study_definition.py
deleted file mode 100644
index c9bb2d9..0000000
--- a/analysis/study_definition.py
+++ /dev/null
@@ -1,17 +0,0 @@
-# Note: If you are using cohortextrator to define your study population you need to
-# (1) delete the ehrQL action in the project.yaml file (lines 14-18) and
-# (2) delete the dataset_definition.py file.
-
-from cohortextractor import StudyDefinition, patients, codelist, codelist_from_csv  # NOQA
-
-
-study = StudyDefinition(
-    default_expectations={
-        "date": {"earliest": "1900-01-01", "latest": "today"},
-        "rate": "uniform",
-        "incidence": 0.5,
-    },
-    population=patients.registered_with_one_practice_between(
-        "2019-02-01", "2020-02-01"
-    ),
-)
diff --git a/project.yaml b/project.yaml
index a369a7d..84a9f6b 100644
--- a/project.yaml
+++ b/project.yaml
@@ -1,18 +1,12 @@
 version: '3.0'
 
+# Ignore this`expectation` block. It is required but not used, and will be removed in future versions.
 expectations:
   population_size: 1000
 
 actions:
-
-  generate_study_population:
-    run: cohortextractor:latest generate_cohort --output-format csv.gz --study-definition study_definition
+  generate_dataset:
+    run: ehrql:v0 generate-dataset analysis/dataset_definition.py --output output/dataset.csv.gz
     outputs:
       highly_sensitive:
-        cohort: output/input.csv.gz
-
-  # generate_dataset:
-  #   run: ehrql:v0 generate-dataset analysis/dataset_definition.py --output output/dataset.csv.gz
-  #   outputs:
-  #     highly_sensitive:
-  #       cohort: output/dataset.csv.gz
+        dataset: output/dataset.csv.gz