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Job request: 679

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study_effectiveness
ID:
uo6rl2dcmpfxkcpc
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

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
        summary3: output/data_summary/type_delivery.txt
        summary4: output/data_summary/type_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
        summarystats: output/data_summary/summary_stats.rds
        summarytables: output/variable_summary/tables/categorical_*.csv


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

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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:06

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

Job request

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-preliminary-study_effectiveness
Requested by
Will Hulme
Branch
effectiveness
Force run dependencies
No
Git commit hash
68f3f89
Requested actions
  • generate_delivery_cohort

Code comparison

Compare the code used in this job request