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Job request: 11536

Organisation:
Bennett Institute
Workspace:
waning-ve-3dose
ID:
thixrjcgovnip72e
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 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 
version: '3.0'

expectations:

  population_size: 100000

actions:

  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## DO NOT EDIT project.yaml 
  ## This file is created by create_project.R 
  ## Edit and run create_project.R to update the project.yaml 
  ## # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # 
  ## #################################### 
  ## study definition 
  ## #################################### 
  ## generate dummy data for study_definition 

  dummy_data_vax:
    run: r:latest analysis/dummy_data_vax.R
    outputs:
      moderately_sensitive:
        dummy_data: analysis/dummy_data_vax.feather

  ## study definition 

  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_vax
      --output-format feather
    dummy_data_file: analysis/dummy_data_vax.feather
    needs:
    - dummy_data_vax
    outputs:
      highly_sensitive:
        cohort: output/input_vax.feather

  ## #################################### 
  ## preprocessing 
  ## #################################### 
  ## process data from study_definition 

  data_input_process:
    run: r:latest analysis/preprocess/input_vax.R
    needs:
    - dummy_data_vax
    - generate_study_population
    outputs:
      highly_sensitive:
        data_wide_vax_dates: output/data/data_wide_vax_dates.rds
        data_processed: output/data/data_processed.rds
      moderately_sensitive:
        data_summaries: output/summaries/data_*.txt

  ## apply eligiblity criteria from box a 

  data_eligible_a:
    run: r:latest analysis/preprocess/data_eligible_a.R
    needs:
    - data_input_process
    outputs:
      highly_sensitive:
        data_eligible_a: output/data/data_eligible_a.rds
      moderately_sensitive:
        eligibility_count_a: output/flow/eligibility_count_a.csv
        group_age_ranges: output/lib/group_age_ranges.csv

  ## #################################### 
  ## plot vaccination dates 
  ## #################################### 

  plot_vax_dates:
    run: r:latest analysis/eda/plot_vax_dates.R
    needs:
    - data_input_process
    - data_eligible_a
    outputs:
      moderately_sensitive:
        vax_date_plots: output/eda/vax_dates*.svg

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:37:35

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

Job request

Status
Succeeded
Backend
TPP
Workspace
waning-ve-3dose
Requested by
Elsie Horne
Branch
main
Force run dependencies
No
Git commit hash
d72023e
Requested actions
  • data_input_process
  • data_eligible_a
  • plot_vax_dates

Code comparison

Compare the code used in this job request