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Job request: 1852

Organisation:
Bennett Institute
Workspace:
post-vax-outcomes-report_main
ID:
5ra74zvy2nhb5ca6
View repo View project.yaml

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

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:

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

Job request

Status
Failed 
JobRequestError: tte_plots failed on a previous run and must be re-run
Backend
TPP
Workspace
post-vax-outcomes-report_main
Requested by
Will Hulme
Branch
master
Force run dependencies
No
Git commit hash
c93b83c
Requested actions
  • run_all

Code comparison

Compare the code used in this job request