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Job request: 4182

Organisation:
Bennett Institute
Workspace:
emis-qa-main
ID:
ulgu7cg5fpftwqo3
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Ben Butler-Cole 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_study_population:
    run: cohortextractor:latest generate_cohort --output-format feather --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.feather

  rotate_study_population:
    run: python:latest python analysis/rotate_study_population.py
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/input-last.feather

  concat_study_populations:
    run: python:latest python analysis/concat_study_populations.py
    needs: [generate_study_population, rotate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/output.feather

  generate_summary_notebook:
    run: python:latest jupyter nbconvert notebooks/summary.ipynb --to=html --output-dir=output/ --execute --ExecutePreprocessor.timeout=86400
    needs: [concat_study_populations]
    outputs:
      moderately_sensitive:
        notebook: output/summary.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:53

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

Job information

Status
Failed
Backend
EMIS
Workspace
emis-qa-main
Requested by
Ben Butler-Cole
Branch
main
Force run dependencies
Yes
Git commit hash
fd1736c
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request