project.yaml

version: "3.0"

expectations:
  population_size: 1000

actions:
  codelist_report_alt:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-alanine-aminotransferase-alt-tests.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/alt
    outputs:
      moderately_sensitive:
        table: output/alt/counts_per_*.csv
        list_sizes: output/alt/list_sizes.csv
        patient_count_table: output/alt/patient_count.csv

  codelist_report_asthma:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-asthma-annual-review-qof.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/asthma
    outputs:
      moderately_sensitive:
        table: output/asthma/counts_per_*.csv
        list_sizes: output/asthma/list_sizes.csv
        patient_count_table: output/asthma/patient_count.csv
  
  codelist_report_cholesterol:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-cholesterol-tests.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/cholesterol
    outputs:
      moderately_sensitive:
        table: output/cholesterol/counts_per_*.csv
        list_sizes: output/cholesterol/list_sizes.csv
        patient_count_table: output/cholesterol/patient_count.csv

  codelist_report_copd:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-chronic-obstructive-pulmonary-disease-copd-review-qof.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/copd
    outputs:
      moderately_sensitive:
        table: output/copd/counts_per_*.csv
        list_sizes: output/copd/list_sizes.csv
        patient_count_table: output/copd/patient_count.csv
  
  codelist_report_hba1c:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-glycated-haemoglobin-hba1c-tests.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/hba1c
    outputs:
      moderately_sensitive:
        table: output/hba1c/counts_per_*.csv
        list_sizes: output/hba1c/list_sizes.csv
        patient_count_table: output/hba1c/patient_count.csv

  codelist_report_medication_review:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-care-planning-medication-review-simple-reference-set-nhs-digital.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/medication_review
    outputs:
      moderately_sensitive:
        table: output/medication_review/counts_per_*.csv
        list_sizes: output/medication_review/list_sizes.csv
        patient_count_table: output/medication_review/patient_count.csv

  codelist_report_qrisk2:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-cvd-risk-assessment-score-qof.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/qrisk2/
    outputs:
      moderately_sensitive:
        table: output/qrisk2/counts_per_*.csv
        list_sizes: output/qrisk2/list_sizes.csv
        patient_count_table: output/qrisk2/patient_count.csv


  codelist_report_rbc:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-red-blood-cell-rbc-tests.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/rbc
    outputs:
      moderately_sensitive:
        table: output/rbc/counts_per_*.csv
        list_sizes: output/rbc/list_sizes.csv
        patient_count_table: output/rbc/patient_count.csv  

  codelist_report_sodium:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-sodium-tests-numerical-value.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/sodium
    outputs:
      moderately_sensitive:
        table: output/sodium/counts_per_*.csv
        list_sizes: output/sodium/list_sizes.csv
        patient_count_table: output/sodium/patient_count.csv

  codelist_report_systolic_bp:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-systolic-blood-pressure-qof.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/systolic_bp
    outputs:
      moderately_sensitive:
        table: output/systolic_bp/counts_per_*.csv
        list_sizes: output/systolic_bp/list_sizes.csv
        patient_count_table: output/systolic_bp/patient_count.csv

  codelist_report_tsh:
    run: >
      cohortextractor:latest generate_codelist_report
        --codelist-path=codelists/opensafely-thyroid-stimulating-hormone-tsh-testing.csv
        --start-date=2019-01-01
        --end-date=2022-11-22
        --output-dir output/tsh
    outputs:
      moderately_sensitive:
        table: output/tsh/counts_per_*.csv
        list_sizes: output/tsh/list_sizes.csv
        patient_count_table: output/tsh/patient_count.csv

  measures:
    run: >
      python:latest python analysis/generate_measures.py
        --input-dir output
        --low-count-threshold 10
        --rounding-base 5
        --rounding-base-practice-count 10
    
    needs: [codelist_report_alt,
            codelist_report_asthma,
            codelist_report_cholesterol,
            codelist_report_copd,
            codelist_report_hba1c,
            codelist_report_medication_review,
            codelist_report_qrisk2,
            codelist_report_rbc,
            codelist_report_sodium,
            codelist_report_systolic_bp,
            codelist_report_tsh]
    outputs:
      moderately_sensitive:
        measure: output/*/measure_counts_per_week_per_practice.csv
        events_count_table: output/*/event_counts.csv
        practice_count_table: output/*/practice_count.csv

  top_5_tables:
    run: >
      python:latest python analysis/top_codes_table.py
        --input-dir output
        --low-count-threshold 10
        --rounding-base 10
    needs: [codelist_report_alt,
            codelist_report_asthma,
            codelist_report_cholesterol,
            codelist_report_copd,
            codelist_report_hba1c,
            codelist_report_medication_review,
            codelist_report_qrisk2,
            codelist_report_rbc,
            codelist_report_sodium,
            codelist_report_systolic_bp,
            codelist_report_tsh,
            measures]
    outputs:
      moderately_sensitive:
        table: output/*/top_5_code_table.csv
  
  
  deciles_charts_alt:
    run: >
      deciles-charts:v0.0.33
        --input-files output/alt/measure_counts_per_week_per_practice.csv
        --output-dir output/alt
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/alt/deciles_*.*
  
  deciles_charts_asthma:
    run: >
      deciles-charts:v0.0.24
        --input-files output/asthma/measure_counts_per_week_per_practice.csv
        --output-dir output/asthma
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/asthma/deciles_*.*

  deciles_charts_cholesterol:
    run: >
      deciles-charts:v0.0.24
        --input-files output/cholesterol/measure_counts_per_week_per_practice.csv
        --output-dir output/cholesterol
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/cholesterol/deciles_*.*

  deciles_charts_copd:
    run: >
      deciles-charts:v0.0.24
        --input-files output/copd/measure_counts_per_week_per_practice.csv
        --output-dir output/copd
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/copd/deciles_*.*

  deciles_charts_hba1c:
    run: >
      deciles-charts:v0.0.24
        --input-files output/hba1c/measure_counts_per_week_per_practice.csv
        --output-dir output/hba1c
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/hba1c/deciles_*.*

  deciles_charts_medication_review:
    run: >
      deciles-charts:v0.0.24
        --input-files output/medication_review/measure_counts_per_week_per_practice.csv
        --output-dir output/medication_review
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/medication_review/deciles_*.*

  deciles_charts_qrisk2:
    run: >
      deciles-charts:v0.0.24
        --input-files output/qrisk2/measure_counts_per_week_per_practice.csv
        --output-dir output/qrisk2
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/qrisk2/deciles_*.*

  deciles_charts_rbc:
    run: >
      deciles-charts:v0.0.24
        --input-files output/rbc/measure_counts_per_week_per_practice.csv
        --output-dir output/rbc
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/rbc/deciles_*.*
  
  deciles_charts_sodium:
    run: >
      deciles-charts:v0.0.24
        --input-files output/sodium/measure_counts_per_week_per_practice.csv
        --output-dir output/sodium
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/sodium/deciles_*.*

  deciles_charts_systolic_bp:
    run: >
      deciles-charts:v0.0.24
        --input-files output/systolic_bp/measure_counts_per_week_per_practice.csv
        --output-dir output/systolic_bp
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/systolic_bp/deciles_*.*

  deciles_charts_tsh:
    run: >
      deciles-charts:v0.0.24
        --input-files output/tsh/measure_counts_per_week_per_practice.csv
        --output-dir output/tsh
    config:
      show_outer_percentiles: true
      tables:
        output: true
      charts:
        output: true
    needs: [measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/tsh/deciles_*.*

  generate_notebook_updating:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/sentinel_measures_updating.ipynb --execute --to html --template basic --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input
    needs:
      [
        measures,
        top_5_tables,
        deciles_charts_alt,
        deciles_charts_asthma,
        deciles_charts_cholesterol,
        deciles_charts_copd,
        deciles_charts_hba1c,
        deciles_charts_medication_review,
        deciles_charts_qrisk2,
        deciles_charts_rbc,
        deciles_charts_sodium,
        deciles_charts_systolic_bp,
        deciles_charts_tsh
      ]
    outputs:
      moderately_sensitive:
        notebook: output/sentinel_measures_updating.html