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Job request: 19574

Organisation:
University of Bristol
Workspace:
covid19-vaccine-uptake-ethnicity-imd
ID:
yp2zq6le434sjae7
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

  • Action:
    kaplan_meier
    Status:
    Status: Succeeded
    Job identifier:
    ddhuhrahzxhe4jze

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000000

actions:
  
  # generate metadata
  design:
    run: r:latest analysis/design.R
    outputs:
      moderately_sensitive:
        lib: analysis/lib/*

  # extract study population
  generate_study_population:
    run: cohortextractor:latest generate_cohort --output-format feather --study-definition study_definition
    needs: 
    - design
    outputs:
      highly_sensitive:
        cohort: output/extract/input.feather

  # generate custom dummy data
  generate_dummy_data:
    run: r:latest analysis/dummy_data.R
    needs:
    - design
    - generate_study_population
    outputs:
      highly_sensitive:
        dummydata: output/extract/dummy_data.feather
        
  process_extract:
    run: r:latest analysis/process_extract.R
    needs:
    - generate_study_population
    - generate_dummy_data
    outputs:
      highly_sensitive:
        data: output/extract/data_eligible.rds
      moderately_sensitive:
        skim: output/extract/skim_*.txt
        flowchart: output/extract/flowchart_*.csv
        
  exploratory_analysis:
    run: r:latest analysis/exploratory_analysis.R
    needs: 
    - process_extract
    outputs:
      moderately_sensitive:
        data_vax_counts: output/exploratory/data_vax_counts_midpoint6.csv
        group_counts: output/exploratory/combined_data_bar_plot_midpoint6.csv
        vax_dates: output/exploratory/vax_dates_*.png
        strat_dist: output/exploratory/strat_dist_*.png

  kaplan_meier:
    run: r:latest analysis/kaplan_meier.R
    needs: 
    - process_extract
    outputs:
      moderately_sensitive:
        vaccine_coverage_all: output/kaplan_meier/vaccine_coverage_all_midpoint6.csv
        km_plot_*: output/kaplan_meier/km_plot_*.png

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:13:51

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid19-vaccine-uptake-ethnicity-imd
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
309d967
Requested actions
  • kaplan_meier

Code comparison

Compare the code used in this Job Request