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Job request: 839

Organisation:
Bennett Institute
Workspace:
covid-vaccine-preliminary-study-master
ID:
b3jhcgtw3bfnr23s
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Brian Mackenna (Gmail) 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:
    generate_delivery_cohort
    Status:
    Status: Failed
    Job identifier:
    g3r2n3riqsvvi4aa
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    35nzipo7orj3t7wi
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_notebook_stp
    Status:
    Status: Failed
    Job identifier:
    dphsa5oqnkqvwwe5
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_report
    Status:
    Status: Failed
    Job identifier:
    qo5uzl2nevtt26po
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_report_stp
    Status:
    Status: Failed
    Job identifier:
    zaztcnnxgy7ho5m2
    Error:
    dependency_failed: Not starting as dependency failed

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
    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 
        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_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

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:12:25

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-master
Requested by
Brian Mackenna (Gmail)
Branch
master
Force run dependencies
No
Git commit hash
7132060
Requested actions
  • generate_delivery_cohort
  • generate_notebook
  • generate_report
  • generate_notebook_stp
  • generate_report_stp

Code comparison

Compare the code used in this job request