Skip to content

Job request: 16199

Organisation:
University of Bristol
Workspace:
vax-fourth-dose-rd
ID:
74xktanyveeg3mcg
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 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.

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: 00:01:35

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

Job request

Status
Succeeded
Backend
TPP
Workspace
vax-fourth-dose-rd
Requested by
Andrea Schaffer
Branch
main
Force run dependencies
No
Git commit hash
6ebfd24
Requested actions
  • cumulative_fourth_dose

Code comparison

Compare the code used in this job request