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Job request: 3211

Organisation:
Bennett Institute
Workspace:
principle_trial_budesonide_inhalers_main
ID:
peoktjrgvhfy6qib
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jon Massey 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: 1000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
  
  generate_notebook:
    run: jupyter:latest jupyter nbconvert  /workspace/analysis/analysis.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400

    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        notebook: output/analysis.html 
          
  input_counts:
      run: python:latest python analysis/input_counts.py
      needs: [generate_study_population]
      outputs:
        moderately_sensitive:
          cohort: output/inputcounts.txt

  generate_study_population_all:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_exclusioncounts
    outputs:
      highly_sensitive:
        cohort: output/input_exclusioncounts.csv

  exclusion_counts:
      run: python:latest python analysis/exclusion_counts.py
      needs: [generate_study_population_all]
      outputs:
        moderately_sensitive:
          cohort: output/exclusioncounts.txt
  
  generate_exclusion_notebook:
    run: jupyter:latest jupyter nbconvert  /workspace/analysis/exclusion_counts.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_study_population_all]
    outputs:
      moderately_sensitive:
        notebook: output/exclusion_counts.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:43:22

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

Job information

Status
Succeeded
Backend
TPP
Workspace
principle_trial_budesonide_inhalers_main
Requested by
Jon Massey
Branch
main
Force run dependencies
No
Git commit hash
a0f4efe
Requested actions
  • generate_exclusion_notebook

Code comparison

Compare the code used in this Job Request