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Job request: 4867

Organisation:
University of Bristol
Workspace:
post-covid-vaccinated
ID:
3rvxibx64mvpihoe
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Venexia Walker 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

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 100000

actions:
  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_electively_unvaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_electively_unvaccinated --output-format feather
    needs: [vax_eligibility_inputs] 
    outputs:
      highly_sensitive:
        cohort: output/input_electively_unvaccinated.feather

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

  generate_study_population_index:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_index --output-format feather
    outputs:
      highly_sensitive:
        cohort: output/input_index.feather

  preprocess_data:
    run: r:latest analysis/preprocess_data.R
    needs: [generate_study_population_index, generate_study_population_vaccinated, generate_study_population_electively_unvaccinated]
    outputs:
      highly_sensitive:
        cohort_vaccinated: output/input_vaccinated.rds
        cohort_electively_unvaccinated: output/input_electively_unvaccinated.rds
        venn_vaccinated: output/venn_vaccinated.rds
        venn_electively_unvaccinated: output/venn_electively_unvaccinated.rds

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 18:19:14

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

Job request

Status
Failed
Backend
TPP
Workspace
post-covid-vaccinated
Requested by
Venexia Walker
Branch
main
Force run dependencies
Yes
Git commit hash
6bb3927
Requested actions
  • run_all

Code comparison

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