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Job request: 4079

Organisation:
University of Manchester
Workspace:
amr-uom-brit-main
ID:
sqm3ggt6g4dyor53
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher ali 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: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to today by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz


  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv
        

  describe:
    run: r:latest analysis/plot/overall_ab_prescribing.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/overall.png
        boxplot: output/overallbox.png

  describe_percentile:
    run: r:latest analysis/plot/overall_ab_prescribing_2575percentile.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        percentile: output/overall_25th_75th_percentile.png

  describe_starpu:
    run: r:latest analysis/plot/starpu_ab_prescribing.R
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        cohort: output/starpuline.png
        boxplot: output/starpubox.png

  describe_infection_event:
    run: r:latest analysis/plot/infection_event_2575percentile.R
    needs: [generate_measures]
    outputs:
       moderately_sensitive:
        percentile1: output/uti_event_25th_75th_percentile.png
        percentile2: output/lrti_event_25th_75th_percentile.png


  describe_infection_ab:
    run: r:latest analysis/plot/infection_ab_boxplot.R
    needs: [generate_study_population]
    outputs:
       moderately_sensitive:
        boxplot1: output/uti_prescribing_rate_box.png
        boxplot2: output/lrti_prescribing_rate_box.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 91:42:03

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

Job request

Status
Failed
Backend
TPP
Workspace
amr-uom-brit-main
Requested by
ali
Branch
main
Force run dependencies
Yes
Git commit hash
40bab54
Requested actions
  • run_all

Code comparison

Compare the code used in this job request