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Job request: 1679

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study-master
ID:
qxs3cpdwvsorkmoj
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 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

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

    needs: [generate_delivery_cohort]
    outputs:
      moderately_sensitive:
        notebook: output/declines.html 
        figures: interim-outputs/declined_vaccines/figures/*
        csvs: machine_readable_outputs/figure_csvs/*
        text: interim-outputs/declined_vaccines/text/*
        
               
#   generate_notebook_stp:
#     run: jupyter:latest jupyter nbconvert /workspace/notebooks/stp_breakdown.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400

#     needs: [generate_delivery_cohort]
#     outputs:
#       moderately_sensitive:
#         notebook: output/stp_breakdown.html
#         figures: interim-outputs/stp/figures/*/*
#         tables: interim-outputs/stp/tables/*
#         text: interim-outputs/stp/text/*
        
        
#   generate_report_stp:
#     run: jupyter:latest jupyter nbconvert /workspace/notebooks/opensafely_vaccine_report_stp.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input

#     needs: [generate_delivery_cohort, generate_notebook_stp]
#     outputs:
#       moderately_sensitive:
#         notebook: output/opensafely_vaccine_report_stp.html 
        
        
#   generate_tables_only_report_stp:
#     run: jupyter:latest jupyter nbconvert /workspace/notebooks/opensafely_tables_only_vaccine_report_stp.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400 --no-input

#     needs: [generate_delivery_cohort, generate_notebook_stp]
#     outputs:
#       moderately_sensitive:
#         notebook: output/opensafely_tables_only_vaccine_report_stp.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:30:59

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccine-preliminary-study-master
Requested by
Helen Curtis
Branch
master
Force run dependencies
No
Git commit hash
c6af698
Requested actions
  • generate_notebook
  • generate_report

Code comparison

Compare the code used in this Job Request