Job request: 271

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher George Hickman requested one or more actions to be run against real patient data in the OpenSAFELY Demo 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
jpi74lbkvbx5zlqm failed generate_cohort_stppop
advb7fejkfynb4rz failed generate_cohort_deaths
5cdtqy5ybl37ihr4 failed generate_cohort_activity
ur6b3xi234ha4ciz failed plot_deaths
xiilmhen2vnsnu4c failed generate_measures_activity
42ocwt4vm2y2fxmq failed plot_activity
atkxnjxagnsz3f43 failed plot_stppop

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 10000

actions:

# actions to plot TPP-STP size

  generate_cohort_stppop:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_1_stppop --output-dir=output/cohorts
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_1_stppop.csv

  plot_stppop:
    run: r:latest analysis/1-plot-stppop.R
    needs: [generate_cohort_stppop]
    outputs:
      moderately_sensitive:
        log: output/logs/log-1-plot-stppop.txt
        figure1: output/plots/plot_stppop_map.png
        figure2: output/plots/plot_stppop_bar.png



# actions to plot deaths over time

  generate_cohort_deaths:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_2_deaths --output-dir=output/cohorts
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_2_deaths.csv

  plot_deaths:
    run: r:latest analysis/2-plot-deaths.R
    needs: [generate_cohort_deaths]
    outputs:
      moderately_sensitive:
        log: output/logs/log-2-plot-deaths.txt
        figure: output/plots/plot_deaths.png

# actions to plot gp activity over time

  generate_cohort_activity:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_3_activity --index-date-range "2020-01-01 to 2020-09-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_3_activity_*.csv

  generate_measures_activity:
    run: cohortextractor:latest generate_measures --study-definition study_definition_3_activity --output-dir=output/measures
    needs: [generate_cohort_activity]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv 

  plot_activity:
    run: r:latest analysis/3-plot-activity.R
    needs: [generate_measures_activity]
    outputs:
      moderately_sensitive:
        log: output/logs/log-3-plot-activity.txt
        figure: output/plots/plot_*.png
       

  run_all:
    needs: [plot_stppop, plot_deaths, plot_activity]
    # In order to be valid this action needs to define a run commmand and
    # some output. We don't really care what these are but the below seems to
    # do the trick.
    run: cohortextractor:latest --version
    outputs:
      moderately_sensitive:
        whatever: project.yaml

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 03:03:47

Config

  • Backend:
    TPP
  • Workspace:
    os-measures-demo
  • Branch:
    master
  • Creator:
    ghickman
  • Force run dependencies:
    True
  • Git Commit Hash:
    89167ff
  • Requested actions:
    • run_all