Skip to content

Job request: 1858

Organisation:
Bennett Institute
Workspace:
post-vax-outcomes-report_main
ID:
4xvffie7orqbonjb
View repo View project.yaml

This page shows the technical details of what happened when authorised researcher Will Hulme 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: 100000

actions:

## Descriptive info on vaccinated patients

  extract_vaccinated:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vaccinated
    outputs:
      highly_sensitive:
        cohort: output/input_vaccinated.csv

  data_process_vaccinated:
    run: r:latest analysis/R/data_process_vaccinated.R
    needs: [extract_vaccinated]
    outputs:
      highly_sensitive:
        cohort: output/data/data_vaccinated.rds
        vaxdates: output/data/data_vaccinated_vax_dates.rds

  data_properties_vaccinated:
    run: r:latest analysis/R/data_properties.R output/data/data_vaccinated.rds output/data_properties
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        summary: output/data_properties/data_vaccinated*.txt

  data_summarise_vaccinated:
    run: r:latest analysis/R/data_summarise.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        summary1: output/variable_summary/categorical.txt
        summary2: output/variable_summary/numeric.txt
        summary3: output/variable_summary/date.txt
        summarytables: output/variable_summary/tables/categorical_*.csv

  vaccine_tables:
    run: r:latest analysis/R/vaccine_type.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        tables: output/vaccine_type/tables/vaccine_type_*.csv

  tte_tables:
    run: r:latest analysis/R/tte_tables.R
    needs: [data_process_vaccinated]
    outputs:
      moderately_sensitive:
        tables: output/tte/tables/event_rates_*.csv

  tte_plots:
    run: r:latest analysis/R/tte_plots.R
    needs: [data_process_vaccinated]
    outputs:
  #    highly_sensitive:
  #      rds: output/tte/figures/plot_*.rds
      moderately_sensitive:
        svg: output/tte/figures/plot_*.svg


  run_markdown:
    run: r:latest -e 'rmarkdown::render("rmarkdown/effectiveness_report.Rmd", knit_root_dir = "/workspace", output_dir="/workspace/output")'
    needs: [data_process_vaccinated, vaccine_tables, tte_tables, tte_plots]
    outputs:
      moderately_sensitive:
        html: output/effectiveness_report.html

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 39:33:55

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

Job information

Status
Succeeded
Backend
TPP
Workspace
post-vax-outcomes-report_main
Requested by
Will Hulme
Branch
master
Force run dependencies
Yes
Git commit hash
c93b83c
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request