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Job request: 7233

Organisation:
Nuffield Trust
Workspace:
deaths-at-home-during-covid-19
ID:
nwvepumn53w56apq
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Eilís Keeble 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: 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: 00:02:51

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

Job information

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