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Job request: 4509

Organisation:
Royal Devon & Exeter NHS Foundation Trust and University of Exeter
Workspace:
sro-gastro
ID:
l3oqzkozxwrqewqk
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Nick Kennedy 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
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  run_model:
    run: r:latest analysis/model.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        count_by_region: output/qfit_by_region.csv
        qfits_by_region: output/qfits_by_region.png
        fobts_by_region: output/fobts_by_region.png
        fobts_by_region_cat: output/fobts_by_region_cat.png
        fobts_by_region_cat_fit: output/fobts_by_region_cat_fit.png
        qfits_by_region_near_10: output/qfits_by_region_near_10.png
        qfit_months_by_region: output/qfit_months_by_region.png
  
  qfit_rmarkdown:
    run: r:latest -e 'rmarkdown::render("analysis/qfit_analysis.Rmd", output_dir = "output")'
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        qfit_html: output/qfit_analysis.html
        
  qfit_region_rmarkdown:
    run: r:latest -e 'rmarkdown::render("analysis/qfit_analysis_region.Rmd", output_dir = "output")'
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        cum_prop_data: output/cum_prop_data.csv
        cum_prop_graph: output/cum_prop_graph.png
        qfit_html: output/qfit_analysis_region.html

  qfit_region_rmarkdown_no_suppress:
    run: r:latest -e 'rmarkdown::render("analysis/qfit_analysis_region.Rmd", output_dir = "output", output_file = "qfit_analysis_region_no_suppress.html", params = list(suppress_if_le = FALSE))'
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        qfit_html: output/qfit_analysis_region_no_suppress.html


  qfit_check_new_data:
    run: r:latest -e 'rmarkdown::render("analysis/check_new_fit_data.Rmd", output_dir = "output")'
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        qfit_html: output/check_new_fit_data.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:18:24

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

Job information

Status
Succeeded
Backend
TPP
Workspace
sro-gastro
Requested by
Nick Kennedy
Branch
main
Force run dependencies
No
Git commit hash
49ec034
Requested actions
  • qfit_region_rmarkdown
  • qfit_region_rmarkdown_no_suppress

Code comparison

Compare the code used in this Job Request