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Job request: 4059

Organisation:
University of Bristol
Workspace:
nhsdtre_replication
ID:
7jvrj53nxga2oqmq
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Venexia Walker requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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_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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 05:16:54

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

Job information

Status
Failed
Backend
TPP
Workspace
nhsdtre_replication
Requested by
Venexia Walker
Branch
main
Force run dependencies
Yes
Git commit hash
c1ed65f
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request