Job request: 8354

View Repo View project.yaml

This page shows the technical details of what happened when authorised researcher Robert Willans requested one or more actions to be run against real patient data in the Impact of the COVID-19 pandemic on anticoagulation for atrial fibrillation project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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

ID Status Action
jg5hheba3m4fuv4d failed generate_report
rqilk3ph5eavffiu failed generate_study_population
dy3gkfyejmtjxrwp failed markdown_doc

Pipeline

Show Hide project.yaml
version: '3.0'

expectations:
  population_size: 20000

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

State

State is inferred from the related Jobs.

Status: Failed

Timings

Timings set to UTC timezone.

  • Created:
  • Started:
  • Finished:
  • Runtime: 00:28:08

Config

  • Backend:
    TPP
  • Workspace:
    nice-audit-lipids2
  • Branch:
    main
  • Creator:
    rwillans
  • Force run dependencies:
    True
  • Git Commit Hash:
    b20adca
  • Requested actions:
    • run_all