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Job request: 8226

Organisation:
Bennett Institute
Workspace:
covid_determinants
ID:
vkanmbp62c3jl6bc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colm Andrews 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: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir=output --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  generate_dataset_report:
    run: >
      dataset-report:v0.0.9
        --input-files output/input.feather
        --output-dir output/
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        dataset_report: output/input.html

  counts:
    run: r:latest analysis/count_tables.r
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        binary_table: output/tables/sex_ethn_binary.csv
        binary_imd_table: output/tables/sex_ethn_binary_imd.csv
        binary_5_table: output/tables/sex_ethn_5.csv
        binary_16_table: output/tables/sex_ethn_16.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:56:14

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid_determinants
Requested by
Colm Andrews
Branch
main
Force run dependencies
Yes
Git commit hash
3d3b310
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request