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Job request: 3385

Organisation:
Bennett Institute
Workspace:
principle_trial_budesonide_inhalers_main
ID:
vyvigfoo2ocb225p
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 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_study_population
    Status:
    Status: Failed
    Job identifier:
    4ba3l6xcxdbi3opq
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    generate_notebook
    Status:
    Status: Failed
    Job identifier:
    vk2w2autth4wop5c
    Error:
    dependency_failed: Not starting as dependency failed

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 

  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: 00:00:06

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

Job request

Status
Failed
Backend
TPP
Workspace
principle_trial_budesonide_inhalers_main
Requested by
Jon Massey
Branch
main
Force run dependencies
No
Git commit hash
d801946
Requested actions
  • generate_study_population
  • generate_notebook

Code comparison

Compare the code used in this job request