Skip to content

Job request: 7232

Organisation:
Nuffield Trust
Workspace:
deaths-at-home-during-covid-19
ID:
rblafqb4hjv67l6q
View repo View project.yaml

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

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  generate_report:
    run: cohort-report:v3.0.0 output/input.feather
    needs: [generate_study_population]
    config:
      output_path: output/cohort_reports_outputs
    outputs: 
      moderately_sensitive:
        report: output/cohort_reports_outputs/descriptives_input.html
        report_charts: output/cohort_reports_outputs/*.png

  describe_cohorts:
    run: r:latest analysis/01_describe_cohorts.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        deaths_cohort: output/describe_cohorts/overall_death_counts/deaths_cohort.csv
        deaths_quarter: output/describe_cohorts/overall_death_counts/deaths_quarter.csv
        deaths_quarter_figure: output/describe_cohorts/overall_death_counts/deaths_quarter.png
        deaths_cohort_pod: output/describe_cohorts/overall_death_counts/deaths_cohort_pod*.csv
        deaths_quarter_pod: output/describe_cohorts/overall_death_counts/deaths_quarter_pod.csv
        deaths_pod_figures: output/describe_cohorts/overall_death_counts/deaths_pod_cohort*.png
        deaths_quarter_characteristic: output/describe_cohorts/quarter_death_counts/deaths_quarter_*.csv
        quarter_summary_table: output/describe_cohorts/quarter_summary_table.csv
        quarter_pod_summary_table: output/describe_cohorts/quarter_pod_summary_table.csv
        deaths_quarter_ons: output/describe_cohorts/ons_death_comparisons/deaths_ons_quarter*.csv
        deaths_month_ons: output/describe_cohorts/ons_death_comparisons/deaths_ons_month*.csv
        deaths_ons_plots: output/describe_cohorts/ons_death_comparisons/deaths_ons*.png
        cohort_summary_table: output/describe_cohorts/cohorts_summary_table.csv
        cohort_pod_summary_table: output/describe_cohorts/cohorts_pod_summary_table*.csv
        death_ratios_cohort: output/describe_cohorts/death_ratios_cohort/death_ratio_cohort*.csv
        death_ratios_pod_cohort: output/describe_cohorts/death_ratios_pod_cohort/death_ratio_pod_cohort*.csv

  describe_service_use:
    run: r:latest analysis/02_describe_service_use.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        service_use_means: output/describe_service_use/service_use_mean*.csv
        gp_complete_service_use_means: output/describe_service_use/complete_gp_history/gp_service_use_mean*.csv
        service_use_ratios: output/describe_service_use/service_use_ratio*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:02:49

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

Job request

Status
Succeeded
Backend
TPP
Workspace
deaths-at-home-during-covid-19
Requested by
Eilís Keeble
Branch
main
Force run dependencies
No
Git commit hash
fe3c10c
Requested actions
  • describe_cohorts
  • describe_service_use

Code comparison

Compare the code used in this job request