Skip to content

Job request: 4175

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
fmlim2vinnfsemes
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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

  • Action:
    counts
    Status:
    Status: Succeeded
    Job identifier:
    j3jlhwht6tmu4de5
  • Action:
    plots
    Status:
    Status: Succeeded
    Job identifier:
    y63sffkrzsaoergh

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output/cohorts --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input.csv.gz

  counts:
    run: r:latest analysis/counts.r
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        death_count: output/tables/death_count.csv.gz
        imd_table: output/tables/imd_count.csv.gz
        age_sex_table: output/tables/age_sex_count.csv.gz
        age_table: output/tables/age_count.csv.gz
        levels: output/tables/levels.RData

  plots:
    run: r:latest analysis/plots.R
    needs: [counts]
    outputs:
      moderately_sensitive:
        figure1: output/plots/Cause_of_Death_count.svg
        figure2: output/plots/imd_count.svg
        figure3: output/plots/age_sex_count.svg
        figure4: output/plots/age_count.svg


  calculate_tpp_coverage:
    run: r:latest analysis/calculate_tpp_coverage.R
    needs: [generate_cohort]
    outputs:
      moderately_sensitive:
        msoa_table: output/tables/tpp_pop_all.csv.gz
        msoa_map: output/plots/tpp_coverage_map.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:05:07

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

Job request

Status
Succeeded
Backend
TPP
Workspace
tpp_representativeness
Requested by
Colm Andrews
Branch
master
Force run dependencies
No
Git commit hash
342a7fe
Requested actions
  • counts
  • plots

Code comparison

Compare the code used in this job request