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Job request: 9193

Organisation:
University of Nottingham
Workspace:
postopcovid
ID:
vjucmkph3b4l7dke
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Colin Crooks 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

  • Action:
    report
    Status:
    Status: Succeeded
    Job identifier:
    tdll53vsyy6rhh2n

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  data_manage:
    run: r:latest analysis/data_manage.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/cohort_long.RData
        
  analysis_crude:
    run: r:latest analysis/analysis_crude.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        km_figures: output/*_km.png
        crude_tables: output/*_counts.csv

  analysis_adjusted:
    run: r:latest analysis/analysis_adjusted.R
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        covid_cox_models: output/*_model.csv
        finalfit_tables: output/*_model.html
        
  report:
    run: r:latest -e 'rmarkdown::render("analysis/Results.rmd", output_dir = "/workspace/output/",knit_root_dir = "/workspace",)'    
    needs: [generate_study_population, data_manage]
    outputs:
      moderately_sensitive:
        results_report: output/Results.html
        bootstrap_km: output/bootstrap.RData

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:37:17

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

Job information

Status
Succeeded
Backend
TPP
Workspace
postopcovid
Requested by
Colin Crooks
Branch
main
Force run dependencies
No
Git commit hash
24f318e
Requested actions
  • report

Code comparison

Compare the code used in this Job Request