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Job request: 762

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_main
ID:
tgqipjdbsqz7bkqa
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:
    kn7a2aodmmymvlm4
  • Action:
    summarise_data
    Status:
    Status: Succeeded
    Job identifier:
    7h7lnon76jc2b6q5
  • Action:
    vaccine_tables
    Status:
    Status: Succeeded
    Job identifier:
    v2wdvkfj5ufy5e6y
  • Action:
    tte_tables
    Status:
    Status: Succeeded
    Job identifier:
    adgq43ejybvtyycb
  • Action:
    tte_plots
    Status:
    Status: Failed
    Job identifier:
    tvmhjehfetb7evvm
    Error:
    nonzero_exit: Job exited with an error code

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:

  extract_data:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.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


  get_packages:
    run: r:latest analysis/R/export_package_names.R
    outputs:    
      moderately_sensitive:
        cohort: output/available_packages.csv

  process_data:
    run: r:latest analysis/R/process_data.R
    needs: [extract_data]
    outputs:
      highly_sensitive:
        cohort1: output/data/data_processed.rds
        cohort2: output/data/data_vaccinated.rds
      moderately_sensitive:
        summary1: output/data_summary/summary_extract.txt
        summary2: output/data_summary/summary_processed.txt
        summary3: output/data_summary/summary_vaccinated.txt
        summary4: output/data_summary/type_extract.txt
        summary5: output/data_summary/type_processed.txt
        summary6: output/data_summary/type_vaccinated.txt


  summarise_data:
    run: r:latest analysis/R/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
        summarytables: output/variable_summary/tables/categorical_*.csv
        summarystats: output/data_summary/summary_stats.json

  vaccine_tables:
    run: r:latest analysis/R/vaccine_type.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        tables: output/vaccine_type/tables/vaccine_type_*.csv

  tte_tables:
    run: r:latest analysis/R/tte_tables.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        tables: output/tte/tables/event_rates_*.csv

  tte_plots:
    run: r:latest analysis/R/tte_plots.R
    needs: [process_data]
    outputs:
      moderately_sensitive:
        plots: output/tte/figures/plot_*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:52:03

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_main
Requested by
Will Hulme
Branch
main
Force run dependencies
No
Git commit hash
59c9f53
Requested actions
  • process_data
  • summarise_data
  • vaccine_tables
  • tte_tables
  • tte_plots

Code comparison

Compare the code used in this job request