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Job request: 6881

Organisation:
NICE
Workspace:
nice-audit-lipids2
ID:
4qj57xdllrslf3bj
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 in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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

  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: 00:29:27

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

Job information

Status
Succeeded
Backend
TPP
Workspace
nice-audit-lipids2
Requested by
Robert Willans
Branch
main
Force run dependencies
No
Git commit hash
146cc39
Requested actions
  • generate_report

Code comparison

Compare the code used in this Job Request