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Job request: 417

Organisation:
Bennett Institute
Workspace:
postcovid-readmission-research_fd_full
ID:
oc7cgobzzbcjub2g
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

  • Action:
    los_plots
    Status:
    Status: Failed
    Job identifier:
    3cv5vvpfbpvp5pdi

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
    outputs:
      highly_sensitive:
        data: output/data/data_processed.rds
        
  make_plots:
    run: r:latest analysis/descriptive-stats.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        plot1: output/figures/plot_dist_age.png
        plot2: 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: 00:00:01

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

Job information

Status
Failed
Backend
TPP
Workspace
postcovid-readmission-research_fd_full
Requested by
Will Hulme
Branch
fd
Force run dependencies
No
Git commit hash
a8c9914
Requested actions
  • los_plots

Code comparison

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