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Job request: 4159

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
latxgygh6iq25zyx
View repo View project.yaml

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

  plots:
    run: r:latest analysis/plots.R
    needs: [counts]
    outputs:
      moderately_sensitive:
        figure1: output/plots/Cause_of_Death.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: 00:02:27

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

Job information

Status
Succeeded
Backend
TPP
Workspace
tpp_representativeness
Requested by
Colm Andrews
Branch
master
Force run dependencies
No
Git commit hash
9ed2418
Requested actions
  • calculate_tpp_coverage

Code comparison

Compare the code used in this Job Request