Job request: 4059

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Venexia Walker requested one or more actions to be run against real patient data in the post-covid-bristol 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

ID Status Action
wh3zjgo4oeutwsrm succeeded generate_study_population
fxc4ndte5catthmv succeeded covariate_check_ages_40_60_80
rzhawwrm4vfmzjuq failed mdl1_unadj
6343x54tas7v66pg failed mdl3b_fullyadj

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  covariate_check_ages_40_60_80:
    run: r:latest analysis/covariate_check.R 40_60_80
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        covariate_check_ages: output/covariate_check_ages_40_60_80.csv

  mdl1_unadj:
      run: r:latest analysis/vw_01_pipe.R mdl1_unadj AMI all
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          tbl_event_count: output/tbl_event_count_mdl1_unadj_infection_AMI_all.csv
          tbl_event_count_red: output/tbl_event_count_red_mdl1_unadj_infection_AMI_all.csv
          tbl_hr: output/tbl_hr_mdl1_unadj_infection_AMI_all.csv

  mdl3b_fullyadj:
      run: r:latest analysis/vw_01_pipe.R mdl3b_fullyadj AMI all
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          tbl_event_count: output/tbl_event_count_mdl3b_fullyadj_infection_AMI_all.csv
          tbl_event_count_red: output/tbl_event_count_red_mdl3b_fullyadj_infection_AMI_all.csv
          tbl_hr: output/tbl_hr_mdl3b_fullyadj_infection_AMI_all.csv

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 05:16:54

Config

  • Backend:
    TPP
  • Workspace:
    nhsdtre_replication
  • Branch:
    main
  • Creator:
    venexia
  • Force run dependencies:
    True
  • Git Commit Hash:
    c1ed65f
  • Requested actions:
    • run_all