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Job request: 12260

Organisation:
Bennett Institute
Workspace:
with_gp_consultations_curation
ID:
46bo4yc55dqsn4wh
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Jon Massey requested one or more actions to be run against real patient data in the 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

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 "2021-01-01 to 2021-12-31 by month"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures
        --study-definition study_definition
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        measure: output/measure_*.csv

  generate_deciles_charts:
    run: deciles-charts:v0.0.33
        --input-files output/measure_*.csv
        --output-dir output/figures
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/figures/deciles_*_*.*
  
  generate_summaries:
    run: python:latest python analysis/summarise.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        measure_totals: output/tables/measure_*_pivot.csv
        overall_summary: output/tables/overall_summary.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 15:49:34

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

Job information

Status
Succeeded
Backend
TPP
Workspace
with_gp_consultations_curation
Requested by
Jon Massey
Branch
main
Force run dependencies
Yes
Git commit hash
e100cd9
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request