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Job request: 2414

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study-master
ID:
uifx3sivursetzw6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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: 50000
    # dummy population size must be at least 50000 to ensure the STP analysis can run successfully
    
actions:

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

#   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 
        figures: interim-outputs/figures/*
        tables: interim-outputs/tables/*
        csvs: machine_readable_outputs/*/* # two possible subfolders
        text: interim-outputs/text/*
        
        
  generate_report:
    run: jupyter:latest env IMAGE_FORMAT=svg jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_overall.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input

    needs: [generate_delivery_cohort, generate_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/opensafely_vaccine_report_overall.html 
        csvs: machine_readable_outputs/table_csvs/*


  generate_simple_report:
    run: jupyter:latest env IMAGE_FORMAT=png jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_overall.ipynb --execute --to html --template basic --output=/workspace/output/opensafely_vaccine_report_overall_simple.html --ExecutePreprocessor.timeout=86400 --no-input

    needs: [generate_delivery_cohort, generate_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/opensafely_vaccine_report_overall_simple.html

        
  generate_report_second_doses:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/second_doses.ipynb --execute --to html --output-dir=/workspace/output/second_doses --ExecutePreprocessor.timeout=86400 --no-input

    needs: [generate_notebook]
    outputs:
      moderately_sensitive:
        notebook: output/second_doses/second_doses.html
        tables: output/second_doses/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:07:26

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-master
Requested by
Helen Curtis
Branch
master
Force run dependencies
No
Git commit hash
07b5788
Requested actions
  • generate_notebook
  • generate_report
  • generate_simple_report
  • generate_report_second_doses

Code comparison

Compare the code used in this job request