project.yaml

version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  # note not possible to execute and save notebook in a single action with `--execute --to notebook` because of self-dependency
  # still possible to execute and save to html or md file

  characteristics_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-patient-characteristics.ipynb --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_population]
    outputs:
      moderately_sensitive:
        html: output/database-patient-characteristics.html

  database_builds_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-builds.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        html: output/database-builds.html
        
  database_schema_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-schema.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        html: output/database-schema.html
       
  characteristics_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-patient-characteristics.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        md: output/database-patient-characteristics.md
       
  database_builds_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-builds.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        md: output/database-builds.md
        png: output/database-builds_files/*.png
        
  database_schema_md:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-schema.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    outputs:
      moderately_sensitive:
        md: output/database-schema.md