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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 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:
    generate_study_population
    Status:
    Status: Succeeded
    Job identifier:
    wh3zjgo4oeutwsrm
  • Action:
    mdl1_unadj
    Status:
    Status: Failed
    Job identifier:
    rzhawwrm4vfmzjuq
    Error:
    No outputs found matching patterns: - output/tbl_event_count_red_mdl1_unadj_infection_AMI_all.csv
  • Action:
    covariate_check_ages_40_60_80
    Status:
    Status: Succeeded
    Job identifier:
    fxc4ndte5catthmv
  • Action:
    mdl3b_fullyadj
    Status:
    Status: Failed
    Job identifier:
    6343x54tas7v66pg
    Error:
    nonzero_exit: Job exited with an error code

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 request

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