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Job request: 5584

Organisation:
Bennett Institute
Workspace:
vaccine-effectiveness-hospital-admissions-validation
ID:
cgkzwv2xrup47sgw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Louis Fisher 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:
    generate_ae_count
    Status:
    Status: Failed
    Job identifier:
    txiiqq4vkclkw6bs
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    generate_events
    Status:
    Status: Succeeded
    Job identifier:
    iaegndvywkaf7pnw
  • Action:
    generate_results
    Status:
    Status: Succeeded
    Job identifier:
    vpt7aywp2vyyln7k

Pipeline

Show project.yaml 
version: "3.0"

expectations:
  population_size: 1000

actions:
  generate_study_population_ae:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_ae
    outputs:
      highly_sensitive:
        cohort: output/input_ae.csv

  generate_ae_count:
    run: python:latest python analysis/ae_count.py
    needs: [generate_study_population_ae]
    outputs:
      moderately_sensitive:
        count: output/ae_count.json
        hospital_count: output/hospital_admission_count.json
        emergency_hospital_count: output/emergency_hospital_admission_count.json
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  generate_events:
    run: python:latest python analysis/events.py
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        ae_events: output/ae_events.feather
        hospital_events: output/hospital_events.feather

  generate_results:
    run: python:latest python analysis/generate_results.py
    needs: [generate_events]
    outputs:
      moderately_sensitive:
        results: output/results_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:56:43

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

Job request

Status
Failed
Backend
TPP
Workspace
vaccine-effectiveness-hospital-admissions-validation
Requested by
Louis Fisher
Branch
master
Force run dependencies
No
Git commit hash
ef07756
Requested actions
  • generate_ae_count
  • generate_events
  • generate_results

Code comparison

Compare the code used in this job request