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Replace cohortextractor with ehrql #110

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Nov 7, 2023
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Replace cohortextractor with ehrql #110

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5 changes: 0 additions & 5 deletions analysis/dataset_definition.py
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Original file line number Diff line number Diff line change
@@ -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

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17 changes: 0 additions & 17 deletions analysis/study_definition.py
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14 changes: 4 additions & 10 deletions project.yaml
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@@ -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
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This is no longer relevant with ehrQL and therefore a source of confusion to have it here. But currently the pipeline validator insists that this be defined for version 3.0 project.yaml files:
https://github.com/opensafely-core/pipeline/blob/8c706d663fb2fcae279bc0f15c1b1b3bd4314e99/pipeline/models.py#L186-L211

So I think we're going to have to move to version 4 for project.yaml files and create a new release of the pipeline library, which is incredibly tedious.

For now, I wonder if we should just stick a comment above this expectations section saying something like "Please ignore this section, it is not used and will be removed in future versions."

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Have created an issue to track this:

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Thanks!


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