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Job request: 515

Organisation:
Bennett Institute
Workspace:
postcovid-readmission-research_fd_full
ID:
b7bz532muhsm7txc
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 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

  • Action:
    process_data
    Status:
    Status: Succeeded
    Job identifier:
    ssowqm2kuirr2dh5

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: 00:00:03

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

Job request

Status
Succeeded
Backend
TPP
Workspace
postcovid-readmission-research_fd_full
Requested by
Will Hulme
Branch
fd
Force run dependencies
No
Git commit hash
860cea2
Requested actions
  • process_data

Code comparison

Compare the code used in this job request