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Job request: 4438

Organisation:
Bennett Institute
Workspace:
tpp_representativeness
ID:
266h6sica66ae5ad
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

  • Action:
    generate_cohort
    Status:
    Status: Succeeded
    Job identifier:
    jrlprawh2lzieusp
  • Action:
    calculate_tpp_coverage
    Status:
    Status: Succeeded
    Job identifier:
    l5bota4zpsreva6o
  • Action:
    counts
    Status:
    Status: Succeeded
    Job identifier:
    pf2qqdr3idpuudwy
  • Action:
    plots
    Status:
    Status: Succeeded
    Job identifier:
    ivbc3ncfjtxwqf5j

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
        imd_table: output/tables/imd_count.csv
        age_sex_table: output/tables/age_sex_count.csv
        age_table: output/tables/age_count.csv
        ethnicity_table: output/tables/ethnic_group.csv


  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
        figure5: output/plots/sex_count.svg
        figure6: output/plots/Cause_of_Death_count_eng.svg
        figure7: output/plots/age_sex_count_eng.svg
        figure8: output/plots/age_count_eng.svg
        figure9: output/plots/sex_count_eng.svg
        figure10: output/plots/ethnicity_count_eng.svg
        figure11: output/plots/ethnicity_count.svg
        figure12: output/plots/ethnicity16_count_eng.svg
        figure13: output/plots/ethnicity16_count.svg

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 03:47:03

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
Yes
Git commit hash
c1aee4f
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request