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Job request: 516

Organisation:
Bennett Institute
Workspace:
postcovid-readmission-research_fd_full
ID:
yohchzfbyeijpfdv
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Will Hulme 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_dummy_population:
  #  run: r:latest analysis/dummy-data.R
  #  outputs:
  #    moderately_sensitive:
  #      dag: output/figures/dag.svg
  #    highly_sensitive:
  #      cohort: output/data/dummy_data.csv

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-dir /output/data
    outputs:
      highly_sensitive:
        cohort: output/data/input.csv

  process_data:
    run: r:latest analysis/process-data.R
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
      moderately_sensitive:
        summary1: output/data-summary/summary_sd.txt 
        summary2: output/data-summary/summary_processed.txt
        
  descriptive:
    run: r:latest analysis/descriptive-stats.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        table1: output/tables/admitted2_reason.csv
        plot1: output/figures/plot_admitted2_reason.png
        plot2: output/figures/plot_dist_age.png
        plot3: output/figures/plot_cmleventrates_sex.png


#  los_plots:
#    run: r:latest analysis/extract-admissions-directly.R
#    outputs:
#      moderately_sensitive:
#        plot1: output/figures/plot_los.png        
#        plot2: output/figures/plot_los_quantiles.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:08

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

Job information

Status
Succeeded
Backend
TPP
Workspace
postcovid-readmission-research_fd_full
Requested by
Will Hulme
Branch
fd
Force run dependencies
Yes
Git commit hash
2ecbf14
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request