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Job request: 3130

Organisation:
Bennett Institute
Workspace:
covid-vaccine-not-done-branch
ID:
mengj77esnry2hep
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  cohort_checks:
    run: python:latest python analysis/cohort_checks.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        cohort: output/cohort_checks.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:
        table: output/*/tables/prevalences.csv

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

  generate_additional_outputs:
    run: python:latest python analysis/run_additional_charts.py
    needs: [transform]
    outputs:
      moderately_sensitive:
        additional_charts: output/*/additional_figures/*.png
        prac_tables: output/*/additional_figures/*.csv

  generate_outputs:
    run: python:latest python analysis/run_charts_and_tables.py
    needs: [transform, compute_uptake_for_paper]
    outputs:
      moderately_sensitive:
        charts: output/*/charts/*.png
        #reports: output/*/reports/*.html
        tables: output/*/tables/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:55

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

Job information

Status
Succeeded
Backend
EMIS
Workspace
covid-vaccine-not-done-branch
Requested by
Helen Curtis
Branch
create-outputs
Force run dependencies
No
Git commit hash
b747464
Requested actions
  • generate_additional_outputs

Code comparison

Compare the code used in this Job Request