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Job request: 445

Organisation:
Bennett Institute
Workspace:
restoration-observatory-emis-research
ID:
bq3daozcr3illw5g
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Jonny Pearson 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

  • Action:
    run_notebook
    Status:
    Status: Succeeded
    Job identifier:
    jhsqhzm7qa3637bu

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  generate_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccine_codelist
    outputs:
      highly_sensitive:
        cohort: output/input_vaccine_codelist.csv

  generate_cohort_2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_target_disease
    outputs:
      highly_sensitive:
        cohort: output/input_target_disease.csv

  # generate_report:
  #   run: python:latest python analysis/report.py output output
  #   needs: [generate_cohort,generate_cohort_2]
  #   outputs:
  #     moderately_sensitive:
  #       report: output/descriptives.html

  run_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/analysis/study_analysis.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_cohort,generate_cohort_2]
    outputs:
      moderately_sensitive:
        notebook: output/study_analysis.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:00:01

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

Job information

Status
Succeeded
Backend
TPP
Workspace
restoration-observatory-emis-research
Requested by
Jonny Pearson
Branch
JPearson_MMR
Force run dependencies
No
Git commit hash
abb8de3
Requested actions
  • run_notebook

Code comparison

Compare the code used in this Job Request