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Job request: 14703

Organisation:
DataLab
Workspace:
sro-key-measures-dashboard
ID:
pzwq2ku4tuot7aje
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Louis Fisher requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show 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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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=2023-01-17
        --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
        table_count: output/*/top_5_code_table_with_count.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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:18:37

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
sro-key-measures-dashboard
Requested by
Louis Fisher
Branch
updating-report-using-interactive
Force run dependencies
No
Git commit hash
b9dc8e0
Requested actions
  • measures
  • 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
  • generate_notebook_updating