Job request: 4588

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, get_practice_count, get_patient_count]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures.html
        subplots: output/sentinel_measures_subplots.png
  

  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