project.yaml

version: '3.0'

expectations:
  population_size: 1000
   
    
actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2021-04-01 by month" --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv
        
  get_patient_count:
    run: python:latest python analysis/get_patients_counts.py
    needs: [generate_study_population]
    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
    outputs:
      highly_sensitive:
        cohort: output/input_ethnicity.csv

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

  generate_study_population_practice_count:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_practice_count --output-dir=output
    outputs:
      highly_sensitive:
        cohort: output/input_practice_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_*.csv

  generate_measure_ethnicity:
    run: python:latest python analysis/generate_measure_ethnicity.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        measure: output/measure_*_ethnicity.csv
  
  get_practice_count:
    run: python:latest python analysis/get_practice_count.py
    needs: [generate_study_population_practice_count]
    outputs:
      moderately_sensitive:
        text: output/practice_count.json
  
  
  
  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
    
  generate_notebook_demographics:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_demographics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs: [generate_measures, get_practice_count, get_patient_count, generate_measure_ethnicity, join_ethnicity]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures_demographics.html
     
  # generate_notebook_practice:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/sentinel_measures_by_practice.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
  #   needs: [generate_measures, get_practice_count, get_patient_count]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/sentinel_measures_by_practice.html
  #       csvs: output/*_check.csv

  get_event_summary:
    run: python:latest python analysis/get_event_summary.py
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        text: output/*_event_summary.csv

  run_tests:
    run: python:latest python -m pytest --junit-xml=output/pytest.xml --verbose
    outputs:
      moderately_sensitive:
        log: output/pytest.xml