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Job request: 194

Organisation:
Bennett Institute
Workspace:
os-measures-demo
ID:
xo2kok6erylnz666
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 within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level the outputs were written to.

The output security levels are:

  • highly_sensitive
    • Researchers can never directly view these outputs
    • Researchers can only request code is run against them
  • moderately_sensitive
    • Can be viewed by an approved researcher by logging into a highly secure environment
    • These are the only outputs that can be requested for public release via a controlled output review service.

Jobs

  • Action:
    plot_activity
    Status:
    Job identifier:
    qyumxq3fdsnkngf5-manually-set

Pipeline

Show 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
        figure: output/plots/plot_stppop.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
        figure1: output/plots/plot_deaths.png
        figure2: output/plots/plot_cmlcoviddeaths_age.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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:31

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

Job request

Status
Succeeded
Backend
TPP
Workspace
os-measures-demo
Requested by
Will Hulme
Branch
master
Force run dependencies
No
Git commit hash
bf51502
Requested actions
  • plot_activity

Code comparison

Compare the code used in this job request