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Job request: 16179

Organisation:
University of Bristol
Workspace:
vax-fourth-dose-rd
ID:
24v3kouquvsr7qmw
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Andrea Schaffer 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 
######################################

# This script defines the project pipeline - it specifies the execution orders for all the code in this
# repo using a series of actions.

######################################


version: '3.0'

expectations:
  population_size: 1000000

actions:

# Generating study population #
  generate_study_pop:
    run: cohortextractor:latest generate_cohort
      --study-definition study_definition_fourth
      --index-date-range "2022-09-02" 
      --output-dir=feather 
      --output-format=feather
    outputs:
      highly_sensitive:
        cohort: output/input_fourth*.feather

# Data processing




# Cumulative uptake of fourth dose #
  cumulative_fourth_dose:
   run: r:latest analysis/descriptive/cumulative_vax_byage.R
   needs: [generate_study_pop]
   outputs:
      moderately_sensitive:
        measure_csv: output/cumulative_rates/final_*.csv
        plot: output/cumulative_rates/plot_*.png

# Flu vaccine uptake #
  # flu_vax:
  #  run: r:latest analysis/descriptive/flu_vax_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/cumulative_rates/flu_*.csv
  #       plot: output/cumulative_rates/plot_flu_vax_byage.png

# Discontinuity of demographics
  # demographics:
  #  run: r:latest analysis/descriptive/demographics_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/variables_by_age/demographics_*.csv
  #       plot: output/variables_by_age/plot_*.png

# Outcome plots #
  # covid_outcomes:
  #  run: r:latest analysis/descriptive/covid_outcomes_byage.R
  #  needs: [generate_study_pop]
  #  outputs:
  #     moderately_sensitive:
  #       measure_csv: output/covid_outcomes/covid_*.csv
  #       plot: output/covid_outcomes/plot_outcomes_*.png
  

# ITT analysis #


# IV analysis #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:44:57

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

Job information

Status
Succeeded
Backend
TPP
Workspace
vax-fourth-dose-rd
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
3cb2d6b
Requested actions
  • generate_study_pop
  • cumulative_fourth_dose

Code comparison

Compare the code used in this Job Request