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Job request: 1597

Organisation:
University of Bristol
Workspace:
vaccine-rd
ID:
zv3f3v2ahibre7hw
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Tom Palmer 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:
    gen_std_popn_3
    Status:
    Status: Failed
    Job identifier:
    gy4apc6tcnqxjiks
  • Action:
    run_model_3
    Status:
    Status: Failed
    Job identifier:
    j63sloacxxk43n5k

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

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

  # run_model:
  #   run: r:latest analysis/1-rcmdbatch.R # 1-basic-rd.R
  #   needs: [gen_std_popn]
  #   outputs:
  #     moderately_sensitive:
  #       figure1: output/plots/pt_plot.png
  #       # figure2: output/plots/four_plot.png
  #       log: logs/1-basic-rd.log

  gen_std_popn_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2
    outputs:
      highly_sensitive:
        cohort: output/input_2.csv

  run_model_2:
    run: r:latest analysis/2-rcmdbatch.R # 2-basic-rd.R
    needs: [gen_std_popn_2]
    outputs:
      moderately_sensitive:
        figure1: output/pt_plot_week_1.png
        figure2: output/pt_plot_week_2.png
        figure3: output/pt_plot_week_3.png
        figure4: output/pt_plot_week_4.png
        figure5: output/pt_plot_week_5.png
        figure6: output/pt_plot_week_6.png
        figure7: output/pt_plot_week_7.png
        figure8: output/pt_plot_week_8.png        
        log: logs/2-basic-rd.log

  gen_std_popn_3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_3
    outputs:
      highly_sensitive:
        cohort: output/input_3.csv

  run_model_3:
    run: r:latest analysis/3-rcmdbatch.R
    needs: [gen_std_popn_3]
    outputs:
      moderately_sensitive:
        log: logs/3-basic-rd.log
  # gen_std_popn_by_week:
  #     run: cohortextractor:latest generate_cohort --study-definition study_definition_2 --index-date-range "2020-12-08 to 2021-02-01 by week" --output-dir=output/measures
  #     outputs:
  #       highly_sensitive:
  #         cohort: output/measures/input_by_week_*.csv
  #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:56:17

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

Job information

Status
Failed
Backend
TPP
Workspace
vaccine-rd
Requested by
Tom Palmer
Branch
main
Force run dependencies
No
Git commit hash
8a50fe1
Requested actions
  • gen_std_popn_3
  • run_model_3

Code comparison

Compare the code used in this Job Request