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Job request: 4340

Organisation:
Bennett Institute
Workspace:
covid-ve-change-over-time--explore-2nd-vax-dates
ID:
wo4rw2gf7ghb4i7g
View repo View project.yaml

This page shows the technical details of what happened when the 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 list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; 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:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    needs: 
    - design
    outputs:
      highly_sensitive:
        cohort: output/input.csv
        
  eda_2nd_vax_dates:
    run: r:latest analysis/explore_2nd_vax_dates.R
    needs:
    - design
    - generate_study_population
    outputs:
      moderately_sensitive:
        data_properties: output/explore_2nd_vax_dates/data/data_processed_tabulate.txt
        plot_data: output/explore_2nd_vax_dates/data/plot_data_redacted.csv

  plot_2nd_vax_dates:
    run: r:latest analysis/plot_2nd_vax_dates.R
    needs:
    - design
    - generate_study_population
    - eda_2nd_vax_dates
    outputs:
      moderately_sensitive:
        plots: output/explore_2nd_vax_dates/images/second_vax_dates_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:26

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--explore-2nd-vax-dates
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
8956269
Requested actions
  • plot_2nd_vax_dates

Code comparison

Compare the code used in this Job Request