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Job request: 2054

Organisation:
Bennett Institute
Workspace:
covid-vaccine-not-done-branch
ID:
w3apjouwo75yykql
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:
    transform
    Status:
    Status: Failed
    Job identifier:
    eqh5pktrdztfj65y
    Error:
    nonzero_exit: Job exited with an error code
  • Action:
    count_prevalences
    Status:
    Status: Failed
    Job identifier:
    c5q2xzasszje34m6
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    compute_uptake_for_paper
    Status:
    Status: Failed
    Job identifier:
    lqds4xkvjfblvwvo
    Error:
    dependency_failed: Not starting as dependency failed

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

  cohort_checks:
    run: python:latest python analysis/cohort_checks.py
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        cohort: output/cohort_checks.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:
        table: output/*/tables/prevalences.csv

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

  generate_additional_outputs:
    run: python:latest python analysis/run_additional_charts.py
    needs: [transform]
    outputs:
      moderately_sensitive:
        additional_charts: output/*/additional_figures/*.png
        prac_table: output/*/additional_figures/practice_decline_summary.csv

  generate_outputs:
    run: python:latest python analysis/run_charts_and_tables.py
    needs: [transform, compute_uptake_for_paper]
    outputs:
      moderately_sensitive:
        charts: output/*/charts/*.png
        #reports: output/*/reports/*.html
        tables: output/*/tables/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:08:58

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

Job request

Status
Failed
Backend
TPP
Workspace
covid-vaccine-not-done-branch
Requested by
Helen Curtis
Branch
create-outputs
Force run dependencies
No
Git commit hash
b26fe6b
Requested actions
  • transform
  • count_prevalences
  • compute_uptake_for_paper

Code comparison

Compare the code used in this job request