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Job request: 176

Organisation:
Bennett Institute
Workspace:
os-measures-demo
ID:
p2kcos4n3i72bosc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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:


# actions to plot deaths over time

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


  plot_deaths:
    run: r:latest analysis/1-plot-deaths.R
    needs: [generate_cohort_deaths]
    outputs:
      moderately_sensitive:
        log: output/logs/log-1-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_activity --index-date-range "2020-01-01 to 2020-09-01 by month" --output-dir=output/measures
    outputs:
      highly_sensitive:
        cohort: output/measures/input_activity_*.csv

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

  plot_measures:
    run: r:latest analysis/1-plot-measures.R
    needs: [generate_measures_activity]
    outputs:
      moderately_sensitive:
        log: output/logs/log-1-plot-measures.txt
        figure: output/plots/plot_*.png
       

  run_all:
    needs: [plot_measures, plot_deaths]
    # 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

Timeline

  • Created:

  • Started:

  • Runtime:

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Job information

Status
Unknown
Backend
TPP
Workspace
os-measures-demo
Requested by
Will Hulme
Branch
master
Force run dependencies
Yes
Git commit hash
a0b175a
Requested actions
  • plot_deaths

Code comparison

Compare the code used in this Job Request