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Job request: 6207

Organisation:
Bennett Institute
Workspace:
mabs-sus
ID:
oiwozj3lvt3bq654
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: 1000

actions:

  generate_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --output-format 'feather'
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  generate_report:
    run: cohort-report:v3.0.0 output/input.feather
    needs: [generate_population]
    config:
      output_path: output/cohort_reports_outputs
    outputs:
      moderately_sensitive:
        reports: output/cohort_reports_outputs/descriptives_input.html
        
  # note not possible to execute and save notebook in a single action with `--execute --to notebook` because of self-dependency
  # still possible to execute and save to html or md file

  # characteristics_html:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-patient-characteristics.ipynb --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #   needs: [generate_population]
  #   outputs:
  #     moderately_sensitive:
  #       html: output/database-patient-characteristics.html

  # database_builds_html:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-builds.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #   outputs:
  #     moderately_sensitive:
  #       html: output/database-builds.html
        
  # database_schema_html:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-schema.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #   outputs:
  #     moderately_sensitive:
  #       html: output/database-schema.html
       
  # characteristics_md:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-patient-characteristics.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #   outputs:
  #     moderately_sensitive:
  #       md: output/database-patient-characteristics.md
       
  # database_builds_md:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-builds.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #   outputs:
  #     moderately_sensitive:
  #       md: output/database-builds.md
  #       png: output/database-builds_files/*.png
        
  # database_schema_md:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/database-schema.ipynb --execute --to markdown --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #   outputs:
  #     moderately_sensitive:
  #       md: output/database-schema.md

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:42:19

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

Job request

Status
Succeeded
Backend
TPP
Workspace
mabs-sus
Requested by
Helen Curtis
Branch
main
Force run dependencies
No
Git commit hash
59141f8
Requested actions
  • generate_population
  • generate_report

Code comparison

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