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Job request: 1134

Organisation:
Bennett Institute
Workspace:
millie_test
ID:
h54f3nbmaj6cv2fx
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green 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

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:
        figure: 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:
        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:
        figure: output/plots/plot_*.png


# alternative stppop anaylsis using better dummy data

  generate_cohort_stppop_map:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_1_stppop_map --output-dir=output/cohorts
    outputs:
      highly_sensitive:
        cohort: output/cohorts/input_1_stppop_map.csv

  plot_stppop_map:
    run: r:latest analysis/1-plot-stppop_map.R
    needs: [generate_cohort_stppop_map]
    outputs:
      moderately_sensitive:
        figure1: output/plots/plot_stppop_bar_names.png
        figure2: output/plots/plot_stppop_map.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:04:27

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

Job request

Status
Succeeded
Backend
TPP
Workspace
millie_test
Requested by
Millie Green
Branch
master
Force run dependencies
Yes
Git commit hash
7be8197
Requested actions
  • plot_stppop

Code comparison

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