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Job request: 5682

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
vaccine-neuro-cohort
ID:
sey26kf5g7wegcxf

This page shows the technical details of what happened when the authorised researcher Anna Schultze 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: 1000

actions:

# EXTRACT DATA FOR EXPOSED AND POTENTIAL CONTROLS 

  ## Extract data on vaccinated people 
  ## NB; This study definition only contains the data needed for matching
  generate_exposed_cohort:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_exposed
    outputs:
      highly_sensitive:
        cohort: output/input_exposed.csv

  ## Extract data on potential concurrent controls 
  generate_concurrent_controls:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_concurrent_controls
    outputs:
      highly_sensitive:
        cohort: output/input_concurrent_controls.csv

  ## Extract data on potential historical controls

# MATCH EXPOSED TO CONTROLS 
# Note that exposed and resulting matches need to_c be extracted into separate csvs to allow appropriate covariate information to be extracted 

  ## Match vaccinated people to concurrent controls 
  match_concurrent:
    run: python:latest python analysis/matching.py
    needs: [generate_exposed_cohort, generate_concurrent_controls]
    outputs:
      moderately_sensitive:
        matching_report: output/matching_report_concurrent.txt
      highly_sensitive:
        matched_cases: output/matched_cases_concurrent.csv
        matched_matches: output/matched_matches_concurrent.csv
        matched_all: output/matched_combined_concurrent.csv

  ## Match vaccinated people to historical controls 

  ## Extract time-dependent data for matched concurrent controls 
  add_covariates_concurrent_controls:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_complete_concurrent 
    needs: [match_concurrent]
    outputs:
      highly_sensitive:
        cohort: output/input_complete_concurrent.csv

  ## Extract time-dependent data for matched historical controls 

# CREATE THE REQUIRED POPULATIONS 
## ie, merge case and match data, apply remaining inclusions and exclusions

  apply_exclusion_criteria:
    run: stata-mp:latest analysis/01_apply_exclusion_criteria.do 
    needs: [add_covariates_concurrent_controls, match_concurrent] 
    outputs:
      moderately_sensitive: 
        log: output/logs/01_apply_exclusion_criteria.log
      highly_sensitive:
        interim_data: output/concurrent_cohort.dta

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 62:55:05

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

Job information

Status
Failed
Backend
TPP
Requested by
Anna Schultze
Branch
main
Force run dependencies
Yes
Git commit hash
86b5cf0
Requested actions
  • run_all

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