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Job request: 25872

Organisation:
UKHSA
Workspace:
study-result-resistant-bsi
ID:
x7tzwvjakhhhdz7p
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Billy Zhong 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: '5.0'

actions:
  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py
         --output output/dataset.csv.gz
    outputs:
      highly_sensitive:
        dataset: output/dataset.csv.gz

  # Step 2a: Sepsis trend analysis (monthly counts, resistant %)
  sepsis_trend_analysis:
    run: r:v2 analysis/sepsis_trend_analysis.R
    needs: [generate_dataset]
    outputs:
      moderately_sensitive:
        table_monthly: output/tables/table_sepsis_monthly.csv
        table_annual: output/tables/table_sepsis_annual.csv
        fig_monthly_trend: output/figures/fig_sepsis_monthly_trend.png
        fig_annual_trend: output/figures/fig_sepsis_annual_trend.png

  # Step 2b: Descriptive analysis
  descriptive_analysis:
    run: r:v2 analysis/descriptive_analysis.R
    needs: [generate_dataset]
    outputs:
      moderately_sensitive:
        table1: output/tables/table1_overall.csv
        table1_period: output/tables/table1_by_period.csv
        table_mortality: output/tables/table_mortality.csv
        table_amr: output/tables/table_amr_codes.csv
        table_covid: output/tables/table_covid_status.csv
        fig_annual: output/figures/fig_cases_by_year.png
        fig_monthly: output/figures/fig_cases_by_year_month.png
        fig_age: output/figures/fig_age_distribution.png
        fig_comorb: output/figures/fig_comorbidity_prevalence.png
        fig_region: output/figures/fig_region_distribution.png
        fig_ethnicity: output/figures/fig_ethnicity_distribution.png
        fig_imd: output/figures/fig_imd_distribution.png
        fig_mortality: output/figures/fig_mortality_by_period.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:15:17

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

Job request

Status
Succeeded
Backend
TPP
Workspace
study-result-resistant-bsi
Requested by
Billy Zhong
Branch
main
Force run dependencies
No
Git commit hash
71545f5
Requested actions
  • generate_dataset

Code comparison

Compare the code used in this job request