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Job request: 1577

Organisation:
University of Bristol
Workspace:
vaccine-rd
ID:
pvfp3ri6zs7b3pkg
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Tom Palmer 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:
    gen_std_popn_3
    Status:
    Status: Succeeded
    Job identifier:
    6smpxcfy6qahj3wh
  • Action:
    run_model_3
    Status:
    Status: Succeeded
    Job identifier:
    nmabzpset42irvv7

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: 01:04:13

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

Job request

Status
Succeeded
Backend
TPP
Workspace
vaccine-rd
Requested by
Tom Palmer
Branch
main
Force run dependencies
No
Git commit hash
2b7d2af
Requested actions
  • gen_std_popn_3
  • run_model_3

Code comparison

Compare the code used in this job request