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Job request: 8474

Organisation:
NICE
Workspace:
nice-audit-lipids2
ID:
et6ru5q4xs4w2nwx
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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 200000

actions:
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.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:
          age: int
          sex: categorical
          CVD_assess_latest_number: float
          CVD_assess_latest_date: date
          CVD_assess_comparator: categorical
          cvdprevent_statins_issued_last_6m: date
          CKD_code: binary
          CVD_code_CVD_prevent: binary
          lipid_modifier_primary: date
          lipid_modifier_secondary: date
          T1D_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: 00:36:18

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

Job request

Status
Succeeded
Backend
TPP
Workspace
nice-audit-lipids2
Requested by
Robert Willans
Branch
main
Force run dependencies
Yes
Git commit hash
000093e
Requested actions
  • generate_study_population
  • markdown_doc

Code comparison

Compare the code used in this job request