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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 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 indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; 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: 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 information

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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