Job request: 1189

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Peter Inglesby requested one or more actions to be run against real patient data in the PRIMIS Covid-19 Vaccine Coverage project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

ID Status Action
bi62ujzfd5q52wbo succeeded generate_study_population
it4dya6kj34pgfhd succeeded transform
zj4ykbr7ggrw3con succeeded count_prevalences
ufi5hmqey4ngcot2 succeeded compute_uptake
wrlhelh7ihnjfrep succeeded report_uptake

Pipeline

Show Hide 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

State

State is inferred from the related Jobs.

Status: Succeeded

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 01:58:04

Config