Skip to content

Job request: 1192

Organisation:
Bennett Institute
Workspace:
primis-covid19-vaccine-uptake-0
ID:
vnxmbi7ilot7ze7l
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Peter Inglesby 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:
    o3vxwxbwx4dnsixx
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    transform
    Status:
    Status: Failed
    Job identifier:
    nxjdt2sap2of5ygu
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    count_prevalences
    Status:
    Status: Failed
    Job identifier:
    ipmkilqhwhgi2vfm
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    compute_uptake
    Status:
    Status: Failed
    Job identifier:
    n4uddqbgucvpo3vn
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    report_uptake
    Status:
    Status: Failed
    Job identifier:
    wyvzgmnka4yjbzvu
    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

  transform:
    run: python:latest python analysis/transform.py output/input.csv
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        cohort: output/cohort.pickle

  count_prevalences:
    run: python:latest python analysis/count_prevalences.py
    needs: [transform]
    outputs:
      moderately_sensitive:
        cohort: output/prevalences_*.pickle

  compute_uptake:
    run: python:latest python analysis/compute_uptake.py
    needs: [transform]
    outputs:
      moderately_sensitive:
        cohort: output/coverage_*.csv

  report_uptake:
    run: python:latest python analysis/report_uptake.py
    needs: [compute_uptake]
    outputs:
      moderately_sensitive:
        report: output/report_*.html
        charts: output/coverage_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:24:30

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

Job request

Status
Failed
Backend
EMIS
Workspace
primis-covid19-vaccine-uptake-0
Requested by
Peter Inglesby
Branch
master
Force run dependencies
Yes
Git commit hash
1a7682b
Requested actions
  • run_all

Code comparison

Compare the code used in this job request