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Job request: 1256

Organisation:
Bennett Institute
Workspace:
primis-codelist-prevalence
ID:
yavdzl7pkb45wqnc
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Helen Curtis 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_notebook
    Status:
    Status: Failed
    Job identifier:
    wnmg3trcjyg3orqt
    Error:
    nonzero_exit: Job exited with an error code

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: 00:03:05

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

Job request

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_notebook

Code comparison

Compare the code used in this job request