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project.yaml
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project.yaml
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version: "3.0"
expectations:
population_size: 1000
actions:
generate_study_population_1:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2019-12-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_*.feather
generate_study_population_2:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2020-01-01 to 2020-12-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input*.feather
generate_study_population_3:
run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2021-01-01 to 2021-06-01 by month" --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/inpu*.feather
get_patient_count:
run: python:latest python analysis/get_patients_counts.py
needs:
[
generate_study_population_1,
generate_study_population_2,
generate_study_population_3,
]
outputs:
moderately_sensitive:
text: output/patient_count.json
generate_study_population_ethnicity:
run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output --output-format=feather
outputs:
highly_sensitive:
cohort: output/input_ethnicity.feather
join_ethnicity:
run: python:latest python analysis/join_ethnicity.py
needs:
[
generate_study_population_1,
generate_study_population_2,
generate_study_population_3,
generate_study_population_ethnicity,
]
outputs:
highly_sensitive:
cohort: output/inp*.feather
get_practice_count:
run: python:latest python analysis/get_practice_count.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
text: output/practice_count.json
generate_measures:
run: cohortextractor:latest generate_measures --study-definition study_definition --output-dir=output
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure_csv: output/measure_*_rate.csv
generate_measures_cleaned:
run: python:latest python analysis/clean_measures.py
needs: [generate_measures]
outputs:
moderately_sensitive:
measure_csv: output/measure_cleaned_*.csv
generate_measures_demographics:
run: python:latest python analysis/calculate_measures.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
measure: output/combined_measure_*.csv
generate_notebook:
run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
needs:
[
generate_measures,
generate_measures_cleaned,
get_practice_count,
get_patient_count,
]
outputs:
moderately_sensitive:
notebook: output/sentinel_measures.html
subplots: output/sentinel_measures_subplots.png
code_tables: output/code_table_*.csv
events_count: output/event_count.json
# generate_notebook_demographics:
# run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures_demographics.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
# needs: [generate_measures, generate_measures_demographics]
# outputs:
# moderately_sensitive:
# notebook: output/sentinel_measures_demographics.html
get_population_count:
run: python:latest python analysis/population_counts.py
needs: [join_ethnicity]
outputs:
moderately_sensitive:
text: output/*_count.csv
demographic_changes:
run: python:latest python analysis/demographic_change.py
needs: [generate_measures_demographics]
outputs:
moderately_sensitive:
csv: output/demographics_differences.csv
csv_sorted: output/demographics_differences_sorted.csv
# run_tests:
# run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
# outputs:
# moderately_sensitive:
# log: output/pytest.xml