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Job request: 10412

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
ra_outcomes
ID:
572okfdh6pk3o35h
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Ruth Costello 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:
  # Study definition for objective 1
  # First for baseline tables
  generate_study_population_monitor_2018:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monitor_bl --index-date-range "2018-03-01"
    outputs:
      highly_sensitive:
        cohort: output/input_monitor_bl_2018-03-01.csv
  
  generate_study_population_monitor_2020:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_monitor_bl --index-date-range "2020-03-23"
    outputs:
      highly_sensitive:
        cohort: output/input_monitor_bl_2020-03-23.csv
  
  # Generate baseline tables
  baseline_monitor:
    run: stata-mp:latest analysis/check.do
    needs: [generate_study_population_monitor_2018, generate_study_population_monitor_2020]
    outputs:
      moderately_sensitive:
        log: logs/baseline.log
  #Study definition for outpatient objective (2)
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition
    outputs:
      highly_sensitive:
        cohort: output/input.csv

  outpatients:
    run: stata-mp:latest analysis/outpatients.do
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        log: logs/outpatients.log
        output: output/tables/op_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 01:35:44

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

Job request

Status
Failed
Backend
TPP
Workspace
ra_outcomes
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
46e1365
Requested actions
  • generate_study_population_monitor_2018
  • generate_study_population_monitor_2020
  • baseline_monitor
  • generate_study_population
  • outpatients

Code comparison

Compare the code used in this job request