project.yaml

version: '3.0'

expectations:
  population_size: 10000

actions:

  # Study populations
  # Extract latests ethnicity record for cohort
  generate_study_population_ethnicity:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_ethnicity 
      --output-dir=output/indicators 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_ethnicity.feather

  # Extract cohort for indicator HYP001 by month 
  generate_study_population_hyp001:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp001 
      --index-date-range "2021-03-01 to 2021-05-01 by month" 
      --output-dir=output/indicators
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp001_*.feather

  # Extract cohort for indicator HYP003 by month 
  generate_study_population_hyp003:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp003 
      --index-date-range "2021-03-01 to 2021-05-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp003_*.feather
  
  # Extract cohort for indicator HYP007 by month 
  generate_study_population_hyp007:
    run: > 
      cohortextractor:latest generate_cohort 
      --study-definition study_definition_hyp007 
      --index-date-range "2021-03-01 to 2021-05-01 by month" 
      --output-dir=output/indicators  
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/indicators/input_hyp007_*.feather

  join_ethnicity:
    run: >
      cohort-joiner:v0.0.27
        --lhs output/indicators/input_hyp*.feather
        --rhs output/indicators/input_ethnicity.feather
        --output-dir output/indicators/joined
    needs: [generate_study_population_ethnicity, generate_study_population_hyp001, generate_study_population_hyp003, generate_study_population_hyp007]
    outputs:
      highly_sensitive:
        cohort: output/indicators/joined/input_hyp*.feather

  # Measures
  # Generate measures for indicator HYP001 by month
  generate_measures_hyp001:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp001 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp001_*_rate.csv

 # Generate measures for indicator HYP003 by month
  generate_measures_hyp003:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp003 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp003_*_rate.csv

  # Generate measures for indicator HYP007 by month
  generate_measures_hyp007:
     run: >
       cohortextractor:latest generate_measures 
       --study-definition study_definition_hyp007 
       --output-dir=output/indicators/joined
     needs: [join_ethnicity]
     outputs:
       moderately_sensitive:
         measure_csv: output/indicators/joined/measure_hyp007_*_rate.csv

  generate_deciles:
    run: >
      deciles-charts:v0.0.21
        --input-files output/indicators/joined/measure_*_*_rate.csv
        --output-dir output/indicators/joined/
    config:
      show_outer_percentiles: false
      tables:
        output: true
      charts:
        output: true
    needs: [generate_measures_hyp001, generate_measures_hyp003, generate_measures_hyp007]
    outputs:
      moderately_sensitive:
        deciles_charts: output/indicators/joined/deciles_chart_*_*_population_rate.png
        deciles_tables: output/indicators/joined/deciles_table_*_*_population_rate.csv
  
  check_data:
    run: r:latest analysis/check_bp_recording_values_dates.R
    needs: [join_ethnicity]
    outputs:
      moderately_sensitive:
        table_count_csv: output/indicators/joined/data_check/tab_hyp*_*_2021_03_01.csv
        skim_txt: output/indicators/joined/data_check/skim_df_hyp*_2021_03_01.txt
        table_date_diff_csv: output/indicators/joined/data_check/tab_hyp*_num_bp_date_diff_2021_03_01.csv
        plot_date_diff: output/indicators/joined/data_check/plot_hyp*_num_bp_date_diff_2021_03_01.png


  # Join all measure files for each indicator
  # join_measures:
  #   run: r:latest analysis/join_measures.R
  #   needs: [generate_measures_hyp001]
  #   outputs:
  #     moderately_sensitive:
  #       measure_csv: output/measures/measures_hyp001.csv