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Job request: 20394

Organisation:
University of Bristol
Workspace:
vaccine-counts
ID:
bswslyjxpwqix3qb
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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

  • Action:
    extract_fixed
    Status:
    Status: Succeeded
    Job identifier:
    ywrmrjb32jdrkapn
  • Action:
    extract_varying
    Status:
    Status: Failed
    Job identifier:
    lwvv33szviz6vchf
  • Action:
    process
    Status:
    Status: Failed
    Job identifier:
    zvwc6lp5mz24ssbu
  • Action:
    report
    Status:
    Status: Failed
    Job identifier:
    vqdr5jyxkrixhgzy

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  extract_fixed:
    run: cohortextractor:latest generate_cohort --output-format feather --study-definition study_definition_fixed
    outputs:
      highly_sensitive:
        cohort: output/input_fixed.feather

  extract_varying:
    run: cohortextractor:latest generate_cohort --output-format feather --study-definition study_definition_varying
    outputs:
      highly_sensitive:
        cohort: output/input_varying.feather


  process:
    run: r:latest analysis/process.R
    needs: [extract_fixed, extract_varying]
    outputs:
      highly_sensitive:
        rds: output/process/*.rds

  report:
    run: r:latest analysis/report.R
    needs: [process]
    outputs:
      moderately_sensitive:
        csv: output/report/*.csv
        png: output/report/*.png

  # Additional actions for snapshot
  extract_snaphot:
    run: >
      cohortextractor:latest generate_cohort
        --study-definition study_definition_snapshot
        --skip-existing
        --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/input_snapshot.csv.gz
        
  process_snapshot:
    run: r:latest analysis/snapshot_process.R
    needs: [extract_snaphot]
    outputs:
      highly_sensitive:
        rds: output/snapshot/processed_snapshot.rds

  report_snapshot:
    run: r:latest analysis/snapshot_report.R
    needs: [process_snapshot]
    outputs:
      moderately_sensitive:
        csv: output/snapshot_report/snapshot*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:39:39

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

Job information

Status
Failed
Backend
TPP
Workspace
vaccine-counts
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
26ea0eb
Requested actions
  • extract_fixed
  • extract_varying
  • process
  • report

Code comparison

Compare the code used in this Job Request