project.yaml

version: "3.0"

expectations:
  population_size: 5000

actions:

  monthly_practice_listsize_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
        --index-date-range '2018-06-01 to 2019-05-31 by month' --output-dir=output/listsize
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/listsize/input_listsize_monthl*.feather

  monthly_practice_listsize_2019:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
        --index-date-range '2019-06-01 to 2020-05-31 by month' --output-dir=output/listsize
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/listsize/input_listsize_month*.feather

  monthly_practice_listsize_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
        --index-date-range '2020-06-01 to 2021-05-31 by month' --output-dir=output/listsize
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/listsize/input_listsize_mont*.feather

  monthly_practice_listsize_2021:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_listsize_monthly
        --index-date-range '2021-06-01 to 2022-12-31 by month' --output-dir=output/listsize
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/listsize/input_listsize_mon*.feather

  monthly_practice_listsize_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_listsize_monthly --output-dir=output/listsize
    needs:
    - monthly_practice_listsize_2018
    - monthly_practice_listsize_2019
    - monthly_practice_listsize_2020
    - monthly_practice_listsize_2021
    outputs:
      moderately_sensitive:
        measure_csv: output/listsize/measure_*.csv


  # Other data
  # ----------
  # Add actions for other data to this section. Prefix them with a suitable name; place
  # scripts in a similarly named sub-directory of the analysis directory; write outputs
  # to a similarly named sub-directory of the output directory.
  #
  # For example, let's call our other data "metrics". We would prefix our actions
  # "metrics_"; we would place our scripts in analysis/metrics; we would write outputs
  # to output/metrics.

  metrics_monthly_sro_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sro_monthly
        --index-date-range '2018-06-01 to 2022-12-31 by month' --output-dir=output/metrics/monthly
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/metrics/monthly/input_sro_monthly*.feather

  metrics_monthly_sro_data_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_sro_monthly --output-dir=output/metrics/monthly
    needs:
    - metrics_monthly_sro_data
    outputs:
      moderately_sensitive:
        measure_csv: output/metrics/monthly/measure_*.csv

  metrics_monthly_kids_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_kids_monthly
        --index-date-range '2018-06-01 to 2022-12-31 by month' --output-dir=output/metrics/monthly
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/metrics/monthly/input_kids_monthly*.feather

  metrics_monthly_kids_data_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition_kids_monthly --output-dir=output/metrics/monthly
    needs:
    - metrics_monthly_kids_data
    outputs:
      moderately_sensitive:
        measure_csv: output/metrics/monthly/measure*.csv

  metrics_generate_deciles_charts:
    run: >
      deciles-charts:v0.0.33
        --input-files output/metrics/monthly/measure_*.csv
        --output-dir output/metrics
    config:
      show_outer_percentiles: true
    needs:
      - metrics_monthly_sro_data_measures
      - metrics_monthly_kids_data_measures
    outputs:
      moderately_sensitive:
        deciles_charts: output/metrics/deciles_chart_*.png
        deciles_tables: output/metrics/deciles_table_*.csv

  metrics_generate_deciles_charts_alternative:
    run: >
      python:latest
        python
        -m analysis.deciles_alternative
        --input-files output/metrics/monthly/measure_*.csv
        --output-dir output/metrics/shaded
    config:
      show_outer_percentiles: true
    needs: 
      - metrics_monthly_sro_data_measures
      - metrics_monthly_kids_data_measures
    outputs:
      moderately_sensitive:
        deciles_charts: output/metrics/shaded/deciles_chart*.png
        deciles_tables: output/metrics/shaded/deciles_table*.csv

  # Metrics data extraction
  # ------------
  metrics_generate_sro_dataset_winter:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
      --param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
      --output-format=feather --output-file output/metrics/input_sro_2021-12-01.feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_sro_2021-12-01.feather

  metrics_generate_sro_dataset_summer:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sro
      --param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
      --output-format=feather --output-file output/metrics/input_sro_2021-06-01.feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_sro_2021-06-01.feather

  metrics_generate_kids_dataset_winter:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
      --param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
      --output-format=feather --output-file output/metrics/input_kids_2021-12-01.feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_kids_2021-12-01.feather

  metrics_generate_kids_dataset_summer:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_kids
      --param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
      --output-format=feather --output-file output/metrics/input_kids_2021-06-01.feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_kids_2021-06-01.feather

  metrics_generate_endpopulation_dataset_winter:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
      --param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/metrics
      --output-format=feather --output-file output/metrics/input_endpopulation_2021-12-01.feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_endpopulation_2021-12-01.feather

  metrics_generate_endpopulation_dataset_summer:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_endpopulation
      --param start_date='2021-06-01' --param end_date='2021-09-30' --output-dir=output/metrics
      --output-format=feather --output-file output/metrics/input_endpopulation_2021-06-01.feather
    outputs:
      highly_sensitive:
        extract: output/metrics/input_endpopulation_2021-06-01.feather

  metrics_generate_sro_measures:
    run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
      --param end_date='2021-09-30' --study-definition study_definition_sro --output-dir=output/metrics
    needs:
    - metrics_generate_sro_dataset_summer
    - metrics_generate_sro_dataset_winter
    outputs:
      moderately_sensitive:
        measure_csv: output/metrics/mea*.csv

  metrics_generate_kids_measures:
    run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
      --param end_date='2021-09-30' --study-definition study_definition_kids --output-dir=output/metrics
    needs:
    - metrics_generate_kids_dataset_summer
    - metrics_generate_kids_dataset_winter
    outputs:
      moderately_sensitive:
        measure_csv: output/metrics/me*.csv

  metrics_generate_endpopulation_measures:
    run: cohortextractor:latest generate_measures --param start_date='2021-06-01'
      --param end_date='2021-09-30' --study-definition study_definition_endpopulation
      --output-dir=output/metrics
    needs:
    - metrics_generate_endpopulation_dataset_summer
    - metrics_generate_endpopulation_dataset_winter
    outputs:
      moderately_sensitive:
        measure_csv: output/metrics/m*.csv

  identify_practices_to_remove:
    run: r:latest analysis/metrics/identify_practices_to_remove.R
    needs:
    - metrics_generate_sro_measures
    - metrics_generate_kids_measures
    - metrics_generate_endpopulation_measures
    outputs:
      highly_sensitive:
        csv: output/metrics/practices_to_remove.csv

  metrics_create_seasonal_data:
    run: r:latest analysis/metrics/create_seasonal_data.R
    needs:
    - metrics_generate_sro_measures
    - metrics_generate_kids_measures
    outputs:
      highly_sensitive:
        csv: output/metrics/season_data_*.csv

  metrics_create_seasonal_measures:
    run: r:latest analysis/metrics/seasonal_measures.R
    needs:
    - metrics_create_seasonal_data
    - appointments_generate_seasonal_summaries_by_booked_month
    - appointments_generate_seasonal_summaries_by_start_month
    - identify_practices_to_remove
    outputs:
      moderately_sensitive:
        raw_csv: output/*/*/summer_winter_all_metrics.csv
        plot_csv: output/*/*/summer_winter_*_histogram_data.csv
        plot_png: output/*/*/summer_winter_*_histogram.png
        plot_csv_redacted: output/*/*/redacted/summer_winter_*_histogram_data_redacted.csv
        plot_png_redacted: output/*/*/redacted/summer_winter_*_histogram_redacted.png
        
  # Epi  
  # -----------------
  epi_generate_winter_outcomes:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_epi
        --param start_date='2021-12-01' --param end_date='2022-03-30' --output-dir=output/epi/
        --output-format=feather
    outputs:
      highly_sensitive:
        extract: output/epi/*.feather

  epi_model_irr:
    run: r:latest analysis/epi/model_irr.R
    needs: 
      - epi_generate_winter_outcomes
      - classify_practices_by_decile
    outputs:
      moderately_sensitive:
        data: output/epi/irr_data.csv
  
  epi_plot_irr:
    run: r:latest analysis/epi/plot_irr.R
    needs: 
      - epi_model_irr
    outputs:
      moderately_sensitive:
        single_plots: output/epi/plots/*.png
        combined_plots: output/epi/plots/combined/*.png


  # Appointments data
  # -----------------
  appointments_generate_dataset_sql:
    run: >
      sqlrunner:latest
        analysis/appointments/dataset_query.sql
        --output output/appointments/dataset_long.csv.gz
        --dummy-data-file analysis/appointments/dummy_dataset_long.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/appointments/dataset_long.csv.gz
        

  appointments_generate_monthly_measures_by_booked_month:
    run: >
      python:latest
        python
        -m analysis.appointments.generate_appointment_monthly_measures
        --value-thresholds 0 2
        --index-cols booked_month practice
    needs: [appointments_generate_dataset_sql]
    outputs:
      highly_sensitive:
        monthly_measure: output/appointments/measure_monthly_*_by_booked_month.csv


  appointments_generate_monthly_measures_by_start_month:
    run: >
      python:latest
        python
        -m analysis.appointments.generate_appointment_monthly_measures
        --value-thresholds 0 2
        --index-cols start_month practice
    needs: [appointments_generate_dataset_sql]
    outputs:
      highly_sensitive:
        monthly_measure: output/appointments/measure_monthly_*_by_start_month.csv

  calculate_total_num_appointments_monthly:
    run: r:latest analysis/calculate_monthly_counts.R
    needs:
      - appointments_generate_monthly_measures_by_booked_month
      - appointments_generate_monthly_measures_by_start_month
    outputs:
      moderately_sensitive:
        overall_csvs: output/appointments/measure_monthly_overall_*.csv
  
  appointments_generate_seasonal_summaries_by_start_month:
    run: >
      python:latest
        python
        -m analysis.appointments.generate_appointment_seasonal_summaries
        --value-thresholds 0 2
        --start-date 2021-06-01
        --end-date 2022-03-31
        --index-cols start_month practice
    needs: [appointments_generate_dataset_sql]
    outputs:
      highly_sensitive:
        monthly_measure: output/appointments/measure_seasonal_*_by_start_month.csv


  appointments_generate_seasonal_summaries_by_booked_month:
    run: >
      python:latest
        python
        -m analysis.appointments.generate_appointment_seasonal_summaries
        --value-thresholds 0 2
        --start-date 2021-06-01
        --end-date 2022-03-31
        --index-cols booked_month practice
    needs: [appointments_generate_dataset_sql]
    outputs:
      highly_sensitive:
        monthly_measure: output/appointments/measure_seasonal_*_by_booked_month.csv

  ### Some of the measures need to be normalised by list size, specifically
  ### anything that starts with 'measure_monthly_num'
  appointments_generate_normalised_counts:
    run: r:latest analysis/normalise_counts.R
    needs:
      - appointments_generate_monthly_measures_by_booked_month
      - appointments_generate_monthly_measures_by_start_month
      - monthly_practice_listsize_measures
    outputs:
      highly_sensitive:
        normalised_csvs: output/appointments/measure_monthly_normalised_*.csv
      moderately_sensitive:
        check_csvs: output/check/*CHECK.csv

  appointments_generate_deciles_charts:
    run: >
      deciles-charts:v0.0.33
        --input-files output/appointments/measure_monthly_*.csv
        --output-dir output/appointments
    config:
      show_outer_percentiles: true
    needs:
      - appointments_generate_monthly_measures_by_booked_month
      - appointments_generate_monthly_measures_by_start_month
      - appointments_generate_normalised_counts
    outputs:
      moderately_sensitive:
        deciles_charts: output/appointments/deciles_chart_*.png
        deciles_tables: output/appointments/deciles_table_*.csv


  appointments_generate_deciles_charts_alternative:
    run: >
      python:latest
        python
        -m analysis.deciles_alternative
        --input-files output/appointments/measure_monthly_*.csv
        --output-dir output/appointments/shaded
    config:
      show_outer_percentiles: true
    needs: 
      - appointments_generate_monthly_measures_by_booked_month
      - appointments_generate_monthly_measures_by_start_month
      - appointments_generate_normalised_counts
    outputs:
      moderately_sensitive:
        deciles_charts: output/appointments/shaded/deciles_chart*.png
        deciles_tables: output/appointments/shaded/deciles_table*.csv


  # Combining data
  # -----------------
  combine_seasonal_data:
    run: r:latest analysis/combine_seasonal_data.R
    needs:
    - metrics_create_seasonal_measures
    - appointments_generate_seasonal_summaries_by_booked_month
    - appointments_generate_seasonal_summaries_by_start_month
    outputs:
      moderately_sensitive:
        csv: output/combined/combined_seasonal_data.csv

  classify_practices_by_decile:
      run: r:latest analysis/classify_practices_by_decile.R
      needs:
      - combine_seasonal_data
      outputs:
        moderately_sensitive:
          csv: output/combined/combined_seasonal_data_with_deciles.csv

  summarise_seasonal_comparisons:
      run: r:latest analysis/summarise_seasonal_comparisons.R
      needs:
      - combine_seasonal_data
      outputs:
        moderately_sensitive:
          csv: output/combined/seasonal_summaries.csv
          redacted_csv: output/combined/seasonal_summaries_nondisclosive.csv



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

  run_r_tests:
    run: r:latest tests/testthat/run-all.R
    outputs:
      moderately_sensitive:
        log: output/tests/run-all.log

  # Presentations and documents
  # ---------------------------
  generate_preliminary_report:
    run: r:latest -e 'rmarkdown::render("reports/preliminary_report.rmd", output_dir = "/workspace/output/docs", knit_root_dir = "/workspace",)'
    needs: 
      - metrics_create_seasonal_measures
      # - metrics_generate_deciles_charts
      - metrics_generate_deciles_charts_alternative
      # - appointments_generate_deciles_charts
      - appointments_generate_deciles_charts_alternative
      - appointments_generate_seasonal_summaries_by_booked_month
      - appointments_generate_seasonal_summaries_by_start_month
      - summarise_seasonal_comparisons
      - identify_practices_to_remove
      - epi_plot_irr
    outputs:
      moderately_sensitive:
        report: output/docs/preliminary_report.html

  create_release:
    run: r:latest analysis/create_release.R
    needs:
      - generate_preliminary_report
      # - appointments_generate_deciles_charts
      - appointments_generate_deciles_charts_alternative
      # - metrics_generate_deciles_charts
      - metrics_generate_deciles_charts_alternative
      - metrics_create_seasonal_measures
      - summarise_seasonal_comparisons
      - epi_plot_irr
    outputs:
      moderately_sensitive:
        html: output/release/*.html
        txt: output/meta-release/*.txt
        plot_data: output/release/*/*.csv
        plot_png: output/release/*/*.png