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Job request: 16157

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
openprompt_longcovid_vaccines
ID:
pa4jpuo52avne5bz
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Alasdair Henderson 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: 1000

actions:

  generate_dataset_cases:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_cases.py --output output/dataset_cases.csv.gz
    outputs:
      highly_sensitive:
        dataset_cases: output/dataset_cases.csv.gz
  
  generate_dataset_controls:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_controls.py --output output/dataset_controls.csv.gz
    outputs:
      highly_sensitive:
        dataset_controls: output/dataset_controls.csv.gz
  
  generate_dataset_lc_pre_vacc:
    run: >
      databuilder:v0 
        generate-dataset analysis/dataset_definition_longcovid_prevaccine.py --output output/dataset_lc_pre_vacc.csv.gz
    outputs:
      highly_sensitive:
        dataset_controls: output/dataset_lc_pre_vacc.csv.gz
  
  # quick_checks: 
  #   run: >
  #     r:latest
  #       analysis/010_quick_checks.R
  #   needs: [generate_dataset_cases, generate_dataset_controls, generate_dataset_lc_pre_vacc]
  #   outputs:
  #      moderately_sensitive:
  #        checks: output/010_quick_checks.html
  
  basic_analysis: 
    run: > 
      r:latest
        analysis/020_longcovidrates.R
    needs: [generate_dataset_cases, generate_dataset_controls, generate_dataset_lc_pre_vacc]
    outputs:
       moderately_sensitive:
         rawrates: output/tab020_raw_lc_rates.csv
         mixmatchrates: output/tab021_raw_lc_rates_mixmatch.csv
         tdcrates:  output/tab022_tdc_lc_rates.csv
         cuminc: output/fig1_cumulative_incidence.pdf
         rawcountsplot: output/fig2_raw_counts_bysex.pdf
         # timeplot:

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 07:50:13

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

Job request

Status
Succeeded
Backend
TPP
Workspace
openprompt_longcovid_vaccines
Requested by
Alasdair Henderson
Branch
main
Force run dependencies
Yes
Git commit hash
62b2c31
Requested actions
  • run_all

Code comparison

Compare the code used in this job request