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Job request: 6895

Organisation:
NICE
Workspace:
nice-audit-lipids2
ID:
iuknykdh3h2hjdhb
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Robert Willans 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:
    wgysciwqgmj5lyqn
  • Action:
    generate_report
    Status:
    Status: Failed
    Job identifier:
    3wsir6njjlkqm2ck
    Error:
    nonzero_exit: Job exited with error code 1
  • Action:
    markdown_doc
    Status:
    Status: Succeeded
    Job identifier:
    w5qboo7d6k7hjlne

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

  report_data:
    run: r:latest analysis/report.R
    needs:
    - generate_study_population
    outputs:
      moderately_sensitive:
        csv: output/report_*.csv
        
  markdown_doc: 
    run:  r:latest -e 'rmarkdown::render("analysis/markdown_report.Rmd", output_dir = "output")'
    needs:  
    - generate_study_population
    outputs:  
      moderately_sensitive:  
        report: output/markdown_report.html

  generate_report:
    run: cohort-report:v3.0.0 output/input.csv
    needs: [generate_study_population]
    config:
      variable_types:
          CVD_assess_latest_date: date
          statins_prescribed: date
          age: int
          sex: categorical
          CVD_assess_latest_number: float
          CVD_assess_comparator: categorical
          CKD_code: binary
          CVD_code: binary
          T1D_code: binary
          T2D_code: binary
          Overall_diab_code: binary
      output_path: output/cohort_reports_outputs
    outputs:
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input.html
        reports_charts: output/cohort_reports_outputs/*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 10:17:08

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

Job request

Status
Failed
Backend
TPP
Workspace
nice-audit-lipids2
Requested by
Robert Willans
Branch
main
Force run dependencies
Yes
Git commit hash
e16b724
Requested actions
  • generate_study_population
  • markdown_doc
  • generate_report

Code comparison

Compare the code used in this job request