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Job request: 4410

Organisation:
University of Bristol
Workspace:
covid-ve-change-over-time-main
ID:
e2pmrwjwvgem4tsh
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Elsie Horne requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the indicated Requested Actions with the Pipeline section below, you can infer what security level various outputs were written to. Outputs marked as highly_sensitive can never be viewed directly by a researcher; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 10000

actions:

  design:
    run: r:latest analysis/design.R
    outputs:
      highly_sensitive:
        study_dates_json: output/lib/study_dates.json
        study_dates_rds: output/lib/study_dates.rds
        jcvi_groups: output/lib/jcvi_groups.csv
        elig_dates: output/lib/elig_dates.csv

  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax --output-format feather
    needs: 
    - design
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather
        
  data_vax_process:
    run: r:latest analysis/eda_index_dates/data_vax_process.R
    needs:
    - design
    - generate_study_population_vax
    outputs:
      highly_sensitive:
        data_2nd_dose: output/eda_index_dates/data/data_2nd_dose.rds
        vax_data: output/data/data_*_vax_dates.rds
      moderately_sensitive:
        data_properties: output/data/data_vax_processed_tabulate.txt

  data_vax_plot:
    run: r:latest analysis/eda_index_dates/data_vax_plot.R
    needs:
    - data_vax_process
    outputs:
      highly_sensitive:
        plot_data: output/eda_index_dates/data/data_vax_plot.rds

  plot_2nd_vax_dates:
    run: r:latest analysis/eda_index_dates/plot_2nd_vax_dates.R
    needs:
    - design
    - data_vax_plot
    outputs:
      moderately_sensitive:
        plots_by_region: output/eda_index_dates/images/plot_by_region_*.png
        plots_all: output/eda_index_dates/images/plot_all_*.png
        second_vax_period_dates: output/lib/second_vax_period_dates.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 10:20:48

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-ve-change-over-time-main
Requested by
Elsie Horne
Branch
main
Force run dependencies
Yes
Git commit hash
ea35897
Requested actions
  • run_all

Code comparison

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