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project.yaml
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project.yaml
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version: '3.0'
expectations:
population_size: 10000
actions:
generate_study_population:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-10-01 to 2021-10-08 by week" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_*.feather
generate_report:
run: cohort-report:v3.0.0 output/input_2021-10-01.feather
needs: [generate_study_population]
config:
output_path: output/cohort_reports_outputs
outputs:
moderately_sensitive:
reports: output/cohort_reports_outputs/descriptives_input_2021-10-01.html
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [generate_study_population]
outputs:
moderately_sensitive:
measure_csv_1: output/measure_*_rate.csv
measure_csv_2: output/measure_*_rate_by_region.csv
measure_csv_3: output/measure_*_rate_by_comparator.csv
measure_csv_4: output/measure_*_rate_by_value.csv
# note the weekly files are not stored, only the compiled file
calculate_rates:
run: python:latest python analysis/rate_calculations.py
needs: [generate_measures]
outputs:
moderately_sensitive:
tables: output/*_per_test.csv
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/SRO_Notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [create_notebook, calculate_rates, generate_study_population_practice_count]
# outputs:
# moderately_sensitive:
# notebook: output/SRO_Notebook.html
# run_tests:
# run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
# outputs:
# moderately_sensitive:
# log: output/pytest.xml