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Job request: 7931

Organisation:
Bennett Institute
Workspace:
mabs-sus
ID:
hxnf5pzilkyqsowt
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Simon Davy 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_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format 'feather'
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  generate_report:
    run: cohort-report:v3.0.0 output/input.feather
    needs: [generate_population]
    config:
      output_path: output/cohort_reports_outputs
    outputs:
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input.html

  summary_html:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/data_summary.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --debug
    needs: [generate_population]
    outputs:
      moderately_sensitive:
        html: output/data_summary.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 11:26:20

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

Job information

Status
Failed
Backend
TPP
Workspace
mabs-sus
Requested by
Simon Davy
Branch
main
Force run dependencies
No
Git commit hash
dd8cabc
Requested actions
  • generate_population

Code comparison

Compare the code used in this Job Request