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Job request: 10359

Organisation:
The London School of Hygiene & Tropical Medicine
Workspace:
ra_outcomes
ID:
opqy5q3txnabqjvb
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 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

  • Action:
    run_all
    Status:
    Status: Succeeded
    Job identifier:
    omnsb4jcmqxfemm6

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:

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

Job information

Status
Succeeded
Backend
TPP
Workspace
ra_outcomes
Requested by
Ruth Costello
Branch
main
Force run dependencies
No
Git commit hash
46e1365
Requested actions
  • run_all

Code comparison

Compare the code used in this Job Request