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Job request: 1121

Organisation:
Bennett Institute
Workspace:
primis-covid19-vaccine-uptake-0
ID:
2rr2hwgudzwphpvh
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:
    transform
    Status:
    Status: Failed
    Job identifier:
    ocqrxjfd752mfhcu
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    count_prevalences
    Status:
    Status: Failed
    Job identifier:
    ky7e2qrxshoc64pp
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    compute_uptake
    Status:
    Status: Failed
    Job identifier:
    fftud4w6s476c2n2
    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/uptake_*.pickle

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:07:40

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

Job request

Status
Failed
Backend
TPP
Workspace
primis-covid19-vaccine-uptake-0
Requested by
Peter Inglesby
Branch
master
Force run dependencies
No
Git commit hash
017f78e
Requested actions
  • transform
  • count_prevalences
  • compute_uptake

Code comparison

Compare the code used in this job request