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Job request: 4684

Organisation:
University of Bristol
Workspace:
covid-ve-change-over-time-main
ID:
m7ai677ti6p2un3k
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Elsie Horne 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: 100000

actions:

  ##########################################################################
  #### preliminaries
  ##########################################################################
  # study parameters ----
  design:
    run: r:latest analysis/design.R
    outputs:
      highly_sensitive:
        study_dates_json: output/lib/study_parameters.json
        study_dates_rds: output/lib/study_parameters.rds
        jcvi_groups: output/lib/jcvi_groups.csv
        elig_dates: output/lib/elig_dates.csv
        regions: output/lib/regions.csv

  ##########################################################################
  #### data for eligibility criteria and vaccines
  ##########################################################################
  # generate dummy data for study_definition_vax ----      
  dummy_data_vax:
    run: r:latest analysis/vax/dummy_data_vax.R
    needs: [design]
    outputs:
      highly_sensitive:
        dummy_data_vax: analysis/vax/dummy_data_vax.feather

  # study definition for eligiblity criteria and vaccine data ----  
  generate_study_population_vax:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax --output-format feather
    dummy_data_file: analysis/vax/dummy_data_vax.feather
    needs: [design, dummy_data_vax]
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather
        
  # process data from study_definition_vax ----  
  data_vax_process:
    run: r:latest analysis/vax/data_vax_process.R
    needs: [design, dummy_data_vax, generate_study_population_vax]
    outputs:
      highly_sensitive:
        data_eligible_a: output/vax/data/data_eligible_a.rds
        data_eligible_b: output/vax/data/data_eligible_b.rds
        vax_data: output/vax/data/data_*_vax_dates.rds
        group_age_ranges: output/lib/group_age_ranges.rds
      moderately_sensitive:
        data_properties: output/vax/data_vax_processed_tabulate.txt
        eligibility_count: output/vax/eligibility_count.csv
        group_age_ranges_csv: output/lib/group_age_ranges.csv

  ##########################################################################
  #### identify second vaccination time periods
  ##########################################################################
  # create dataset for identifying second vaccination time periods ----  
  data_vax_plot:
    run: r:latest analysis/second_vax_period/data_vax_plot.R
    needs: [design, data_vax_process]
    outputs:
      highly_sensitive:
        data_moving_average: output/second_vax_period/data/data_ma.rds
      moderately_sensitive:
        second_vax_period_dates: output/lib/second_vax_period_dates.csv
        start_dates: output/lib/start_dates.csv
        end_dates: output/lib/end_dates.csv

  # identify and plot second vaccination time periods ----  
  plot_2nd_vax_dates:
    run: r:latest analysis/second_vax_period/plot_2nd_vax_dates.R
    needs: [design, data_vax_process, data_vax_plot]
    outputs:
      moderately_sensitive:
        plots_by_region: output/second_vax_period/images/plot_by_region_*.png

  ##########################################################################
  #### data for covariates
  ##########################################################################
    # generate dummy data for study_definition_vax ----      
  dummy_data_covs:
    run: r:latest analysis/covs/dummy_data_covs.R
    needs: [design, dummy_data_vax, data_vax_plot]
    outputs:
      highly_sensitive:
        dummy_data_vax: analysis/covs/dummy_data_covs.feather

  # study definition for covariates ----  
  generate_study_population_covs:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_covs --output-format feather
    dummy_data_file: analysis/covs/dummy_data_covs.feather
    needs: [design, data_vax_plot, dummy_data_covs]
    outputs:
      highly_sensitive:
        cohort: output/input_covs.feather

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:23:18

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

Job information

Status
Succeeded
Backend
TPP
Workspace
covid-ve-change-over-time-main
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
7cfd4cd
Requested actions
  • data_vax_process

Code comparison

Compare the code used in this Job Request