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Job request: 1234

Organisation:
Bennett Institute
Workspace:
primis-covid19-vaccine-uptake-0
ID:
mk4ux6m7yndwo6ux
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Peter Inglesby 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
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  transform:
    run: python:latest python analysis/transform.py output/input.csv
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/cohort.pickle

  # count_prevalences:
  #   run: python:latest python analysis/count_prevalences.py
  #   needs: [transform]
  #   outputs:
  #     moderately_sensitive:
  #       cohort: output/prevalences_*.pickle

  # compute_uptake:
  #   run: python:latest python analysis/compute_uptake.py
  #   needs: [transform]
  #   outputs:
  #     moderately_sensitive:
  #       cohort: output/coverage_*.csv

  # report_uptake:
  #   run: python:latest python analysis/report_uptake.py
  #   needs: [compute_uptake]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/report_*.html
  #       charts: output/coverage_*.png

  compute_uptake_for_paper:
    run: python:latest python analysis/compute_uptake_for_paper.py
    needs: [transform]
    outputs:
      moderately_sensitive:
        cohort: output/*/paper/*/*.csv

  compute_more_uptake_for_paper:
    run: python:latest python analysis/compute_more_uptake_for_paper.py
    needs: [transform]
    outputs:
      moderately_sensitive:
        cohort: output/*/paper/all/wave.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:31

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

Job information

Status
Succeeded
Backend
TPP
Workspace
primis-covid19-vaccine-uptake-0
Requested by
Peter Inglesby
Branch
master
Force run dependencies
No
Git commit hash
32e3ac9
Requested actions
  • compute_more_uptake_for_paper

Code comparison

Compare the code used in this Job Request