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Job request: 1254

Organisation:
Bennett Institute
Workspace:
primis-codelist-prevalence
ID:
nwf4kddfamkipclp
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: 10000

actions:

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  generate_study_population_with_codes:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_with_codes
    outputs:
      highly_sensitive:
        cohort: output/input_with_codes.csv


  generate_notebook:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/prevalence_comparison.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        notebook: output/prevalence_comparison.html 
        table: safe-outputs/*
        
        
  generate_notebook_code_comparison:
    run: jupyter:latest jupyter nbconvert /workspace/notebooks/prevalence_deepdive.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
    needs: [generate_study_population_with_codes]
    outputs:
      moderately_sensitive:
        notebook: output/prevalence_deepdive.html 
        table: safe-outputs/by-codelist/*

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:09:55

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

Job information

Status
Failed
Backend
EMIS
Workspace
primis-codelist-prevalence
Requested by
Helen Curtis
Branch
master
Force run dependencies
No
Git commit hash
82655b0
Requested actions
  • generate_study_population_with_codes
  • generate_notebook
  • generate_notebook_code_comparison

Code comparison

Compare the code used in this Job Request