project.yaml

version: "3.0"

expectations:
  population_size: 15000

actions:
  generate_study_population_monitoring:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monitoring --index-date-range "2019-01-01 to 2021-12-01 by month" --output-dir=output --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/input_monitoring_*.csv

  generate_measures_monitoring:
    run: cohortextractor:latest generate_measures --study-definition study_definition_monitoring --output-dir=output
    needs: [generate_study_population_monitoring]
    outputs:
      moderately_sensitive:
        measure_csv: output/measure_monitoring_*_rate.csv

  generate_study_population_ethnicity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ethnicity --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-12-01 by month" --output-dir=output --skip-existing
    outputs:
      highly_sensitive:
        cohort: output/input*.csv

  join_ethnicity:
    run: python:latest python analysis/join_ethnicity.py
    needs: [generate_study_population, generate_study_population_ethnicity]
    outputs:
      highly_sensitive:
        cohort: output/in*.csv

  patient_count:
    run: python:latest python analysis/get_patient_count.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        csv: output/patient_count.csv

  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_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/notebook.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [join_ethnicity, generate_measures, generate_measures_monitoring]
    outputs:
      moderately_sensitive:
        notebook: output/notebook.html
        figures: output/measure_*.jpeg
        total_csv: output/doac_rate_total.csv
        csvs: output/current_doac_*.csv
        self_monitoring: output/self_monitoring_current.csv
        blood_monitoring: output/blood_monitoring_current.csv

  recent_data:
    run: python:latest python analysis/recent_data.py
    needs: [generate_notebook]
    outputs:
      moderately_sensitive:
        csv: output/doac_rate_total_recent.csv

  # # to be run locally
  # combine:
  #   run: python:latest python analysis/combined_analysis.py
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: released_outputs/combined_rate.csv
  #       count: released_outputs/count.jpeg
  #       count_with_mean: released_outputs/count_with_mean.jpeg
  #       rate: released_outputs/rate.jpeg

  # # # to be run locally
  # generate_report_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/analysis/report_notebook.ipynb --execute --to html --output-dir=/workspace/released_outputs --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [combine]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: released_outputs/report_notebook.html