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Job request: 10648

Organisation:
Royal Devon & Exeter NHS Foundation Trust and University of Exeter
Workspace:
sro-gastro
ID:
yv36pau6bqxz66vm
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: Failed
    Job identifier:
    eduyewy7sgbdw5zj
    Error:
    cancelled_by_user: Cancelled by user
  • Action:
    qfit_region_rmarkdown
    Status:
    Status: Failed
    Job identifier:
    dhczbpbevedplnz7
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    qfit_region_rmarkdown_no_suppress
    Status:
    Status: Failed
    Job identifier:
    azhvrjxk5m25k6rr
    Error:
    dependency_failed: Not starting as dependency failed

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
        cum_prop_data_all_ages: output/cum_prop_data_all_ages.csv
        cum_prop_graph_all_ages: output/cum_prop_graph_all_ages.png
        qfit_html: output/qfit_analysis_region.html
        n_by_region_period: output/n_by_region_period.csv
        n_by_region_month: n_by_region_month.csv

  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: 00:35:46

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
ba838e7
Requested actions
  • generate_study_population
  • qfit_region_rmarkdown
  • qfit_region_rmarkdown_no_suppress

Code comparison

Compare the code used in this job request