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Job request: 10387

Organisation:
University of Bristol
Workspace:
post-covid-gastrointestinal
ID:
gm5luomywyenpgtu
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Marwa Al Arab 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_prelim
    Status:
    Status: Succeeded
    Job identifier:
    je6zkzyj44wli3lf
  • Action:
    generate_index_dates
    Status:
    Status: Failed
    Job identifier:
    ner3bb3cd6s7bpzz
    Error:
    Internal error: this usually means a platform issue rather than a problem for users to fix. The tech team are automatically notified of these errors and will be investigating.
  • Action:
    generate_study_population_vaccinated
    Status:
    Status: Failed
    Job identifier:
    bt5fyf5b7thnsdfb
    Error:
    dependency_failed: Not starting as dependency failed

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 1000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml DIRECTLY 
  ## This file is created by create_project_actions.R 
  ## Edit and run create_project_actions.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 

  vax_eligibility_inputs:
    run: r:latest analysis/vax_eligibility_inputs.R
    outputs:
      highly_sensitive:
        vax_study_dates_json: output/vax_study_dates.json
        vax_jcvi_groups: output/vax_jcvi_groups.csv
        vax_eligible_dates: output/vax_eligible_dates.csv

  generate_study_population_prelim:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_prelim
      --output-format feather
    needs:
    - vax_eligibility_inputs
    outputs:
      highly_sensitive:
        cohort: output/input_prelim.feather

  generate_index_dates:
    run: r:latest analysis/prelim.R
    needs:
    - vax_eligibility_inputs
    - generate_study_population_prelim
    outputs:
      highly_sensitive:
        cohort: output/index_dates.csv

  generate_study_population_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
      --output-format feather
    needs: 
    - generate_index_dates
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.feather

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:43:13

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

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-gastrointestinal
Requested by
Marwa Al Arab
Branch
main
Force run dependencies
Yes
Git commit hash
f3b50d3
Requested actions
  • vax_eligibility_inputs
  • generate_study_population_prelim
  • generate_index_dates
  • generate_study_population_vaccinated

Code comparison

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