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Job request: 3501

Organisation:
Royal Devon & Exeter NHS Foundation Trust and University of Exeter
Workspace:
sro-gastro
ID:
mryeo3jvt66epqi2
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Nick Kennedy 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:
    generate_study_population
    Status:
    Status: Succeeded
    Job identifier:
    vyxpsoihgfnazxwt
  • Action:
    qfit_rmarkdown
    Status:
    Status: Succeeded
    Job identifier:
    j6p5beidzh2gydg2
  • Action:
    qfit_region_rmarkdown
    Status:
    Status: Succeeded
    Job identifier:
    4gmiciuao2jpby65
  • Action:
    run_model
    Status:
    Status: Failed
    Job identifier:
    65mtbl3ybiyhwpt7
    Error:
    No outputs found matching patterns: - output/qfit_by_stp.csv - output/qfits_by_stp.png - output/fobts_by_stp.png - output/fobts_by_stp_cat.png - output/fobts_by_stp_cat_fit.png - output/qfits_by_stp_near_10.png - output/qfit_months_by_stp.png

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_stp: output/qfit_by_stp.csv
        qfits_by_stp: output/qfits_by_stp.png
        fobts_by_stp: output/fobts_by_stp.png
        fobts_by_stp_cat: output/fobts_by_stp_cat.png
        fobts_by_stp_cat_fit: output/fobts_by_stp_cat_fit.png
        qfits_by_stp_near_10: output/qfits_by_stp_near_10.png
        qfit_months_by_stp: output/qfit_months_by_stp.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:
        qfit_html: output/qfit_analysis_region.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:47:04

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

Job request

Status
Failed
Backend
TPP
Workspace
sro-gastro
Requested by
Nick Kennedy
Branch
main
Force run dependencies
No
Git commit hash
9fb66e1
Requested actions
  • generate_study_population
  • run_model
  • qfit_rmarkdown
  • qfit_region_rmarkdown

Code comparison

Compare the code used in this job request