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Job request: 660

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study_effectiveness
ID:
3hrg37vixy2dsven
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:
    tte_plots
    Status:
    Status: Failed
    Job identifier:
    bplpe2774xuebsux
    Error:
    Job exited with an error code
  • Action:
    summarise_data
    Status:
    Status: Succeeded
    Job identifier:
    hog74d2uofo4r6jq

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:

  generate_delivery_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_delivery
    outputs:
      highly_sensitive:
        cohort: output/input_delivery.csv

  generate_eligibility_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_eligibility
    outputs:
      highly_sensitive:
        cohort: output/input_eligibility.csv

  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400

    needs: [generate_delivery_cohort]
    outputs:
      moderately_sensitive:
        notebook: output/population_characteristics.html


  process_data:
    run: r:latest analysis/effectiveness/process_data.R
    needs: [generate_delivery_cohort]
    outputs:
      highly_sensitive:
        cohort: output/data/data_processed.rds
      moderately_sensitive:
        summary1: output/data_summary/summary_delivery.txt
        summary2: output/data_summary/summary_processed.txt


  summarise_data:
    run: r:latest analysis/effectiveness/summarise_data.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        summary1: output/variable_summary/categorical.txt
        summary2: output/variable_summary/numeric.txt
        summary3: output/variable_summary/date.txt


  tte_plots:
    run: r:latest analysis/effectiveness/tte_plots.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        #summary1: output/variable_summary/categorical.txt
        plots: output/figures/time_to_event/plot_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:07

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-vaccine-preliminary-study_effectiveness
Requested by
Will Hulme
Branch
effectiveness
Force run dependencies
No
Git commit hash
84a8202
Requested actions
  • summarise_data
  • tte_plots

Code comparison

Compare the code used in this job request