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Job request: 866

Organisation:
Bennett Institute
Workspace:
covid-vaccineeffectiveness-research_doses
ID:
tmkxjsjt36kl7nlw
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 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:

  # generate_notebook:
  #   run: jupyter:latest jupyter nbconvert /workspace/notebooks/population_characteristics.ipynb --execute --to html --output-dir=/workspace/output --ExecutePreprocessor.timeout=86400
  #
  #   needs: [generate_delivery_cohort]
  #   outputs:
  #     moderately_sensitive:
  #       notebook: output/population_characteristics.html

  get_packages:
    run: r:latest analysis/R/export_package_names.R
    outputs:
      moderately_sensitive:
        cohort: output/available_packages.csv



## 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

  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:
    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
        summarystats: output/summary_stats.json

  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:
      moderately_sensitive:
        plots: output/tte/figures/plot_*.svg


  ## VE in over 80s

  extract_over80s:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_over80s
    outputs:
      highly_sensitive:
        cohort: output/input_over80s.csv


  data_process_over80s:
    run: r:latest analysis/R/data_process_over80s.R
    needs: [extract_over80s]
    outputs:
      highly_sensitive:
        data: output/data/data_*.rds

  data_properties_processed_over80s:
    run: r:latest analysis/R/data_properties.R output/data/data_processed_over80s.rds output/data_properties
    needs: [data_process_over80s]
    outputs:
      moderately_sensitive:
        summary: output/data_properties/data_processed*.txt

  data_properties_tte_over80s:
    run: r:latest analysis/R/data_properties.R output/data/data_tte_over80s.rds output/data_properties
    needs: [data_process_over80s]
    outputs:
      moderately_sensitive:
        summary: output/data_properties/data_tte*.txt


  models_over80s:
    run: r:latest analysis/R/models_over80s.R
    needs: [data_process_over80s]
    outputs:
      moderately_sensitive:
        zph: output/models/figures/zph*.png
        forest: output/models/figures/forest*.png
        tables: output/models/tables/*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:57:06

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-vaccineeffectiveness-research_doses
Requested by
Will Hulme
Branch
doses
Force run dependencies
No
Git commit hash
b6a640d
Requested actions
  • extract_over80s
  • data_process_over80s
  • data_properties_processed_over80s
  • data_properties_tte_over80s
  • models_over80s

Code comparison

Compare the code used in this Job Request