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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_report_ethnicity:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_ethnicity_report --output-dir output/report --output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/report/input_ethnicity_report.csv.gz
### Curation check ###
curation_monthly:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_report
--index-date-range "2019-01-01 to 2019-01-01 by month"
--param frequency=monthly
--output-dir=output/curation
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/curation/input_report_2019-01-01.csv.gz
dataset_report_monthly:
run: python:latest python analysis/dataset_report.py
--input-files output/curation/input_report_2019-01-01.csv.gz
--output-dir output/curation/
--granularity "year"
needs: [curation_monthly]
outputs:
moderately_sensitive:
# Only output the single summary file
cohort_report: output/curation/input_report_2019-01-01.html
curation_weekly:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_report
--index-date-range "2022-07-01 to 2022-07-01 by week"
--param frequency=weekly
--output-dir=output/curation
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/curation/input_report_2022-07-01.csv.gz
dataset_report_weekly:
run: python:latest python analysis/dataset_report.py
--input-files output/curation/input_report_2022-07-01.csv.gz
--output-dir output/curation/
--granularity "day"
needs: [curation_weekly]
outputs:
moderately_sensitive:
# Only output the single summary file
cohort_report: output/curation/input_report_2022-07-01.html
### End curation check
generate_study_population_report_monthly:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_report
--index-date-range "2019-01-01 to 2022-06-01 by month"
--param frequency=monthly
--output-dir=output/report
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/report/input_*-01.csv.gz
generate_study_population_report_weekly:
run: cohortextractor:latest generate_cohort
--study-definition study_definition_report
--index-date-range "2022-07-01 to 2023-01-08 by week"
--param frequency=weekly
--output-dir=output/report
--output-format=csv.gz
outputs:
highly_sensitive:
cohort: output/report/input_*.csv.gz
join_cohorts_report:
run: >
cohort-joiner:v0.0.38
--lhs output/report/input_report_20*.csv.gz
--rhs output/report/input_ethnicity_report.csv.gz
--output-dir output/report/joined
needs: [generate_study_population_report_monthly, generate_study_population_report_weekly, generate_study_population_report_ethnicity]
outputs:
highly_sensitive:
cohort: output/report/joined/input_report_20*.csv.gz
generate_measures_report:
run: cohortextractor:latest generate_measures --study-definition study_definition_report --output-dir=output/report/joined
needs: [join_cohorts_report]
outputs:
moderately_sensitive:
measure_csv: output/report/joined/measure_event_*_rate.csv
join_measures:
run: python:latest python analysis/join_and_round.py
--input-files output/report/joined/measure_*_rate.csv
--output-dir output/report/joined
--output-name "measure_all.csv"
--skip-round
needs: [generate_measures_report]
outputs:
moderately_sensitive:
# Only output the single summary file
measure_csv: output/report/joined/measure_all.csv
top_5_table_report:
run: >
python:latest python analysis/report/top_5_report.py
--input-file output/report/joined/measure_all.csv
--output-dir output/report/joined
needs: [join_measures]
outputs:
moderately_sensitive:
tables: output/report/joined/top_5*.csv
plot_measure_report:
run: >
python:latest python analysis/report/plot_measures_report.py
--measure-path output/report/joined/measure_all.csv
--output-dir output/report/joined
needs: [join_measures]
outputs:
moderately_sensitive:
measure: output/report/joined/*measures*.jpeg
event_counts_report:
run: >
python:latest python analysis/report/event_counts.py --input-dir="output/report/joined" --output-dir="output/report" --measures="amoxicillin,azithromycin,clarithromycin,erythromycin,phenoxymethypenicillin"
needs: [join_cohorts_report]
outputs:
moderately_sensitive:
measure: output/report/event_counts_*.json
# create_notebook:
# run: python:latest python analysis/report/create_notebook.py
# outputs:
# moderately_sensitive:
# notebook: output/report/report.ipynb
# generate_notebook:
# run: jupyter:latest jupyter nbconvert /workspace/output/report/report.ipynb --execute --to html --output-dir=/workspace/output/report --ExecutePreprocessor.timeout=86400 --no-input
# needs: [create_notebook, event_counts_report, deciles_chart_report, top_5_table_report, plot_measure_report]
# outputs:
# moderately_sensitive:
# notebook: output/report/report.html