Skip to content

Job request: 7726

Organisation:
University of Liverpool
Workspace:
avoidable-hospitalisations-trends
ID:
mgl2vr4e2njllzmd
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Mark A Green 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.

Pipeline

Show project.yaml 
version: '3.0'

expectations:
  population_size: 1000

actions:
    
  generate_study_population:
    run: cohortextractor:latest generate_cohort --study-definition study_definition --index-date-range "2019-01-01 to 2022-04-30 by month" --skip-existing --output-dir=output/measures --output-format=csv.gz
    outputs:
      highly_sensitive:
        cohort: output/measures/input_*.csv.gz

  generate_measures:
    run: cohortextractor:latest generate_measures --study-definition study_definition --skip-existing --output-dir=output/measures
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        measure_csv: output/measures/measure_*.csv

  process_data:
    run: r:latest analysis/create_age_standardised_outputs.R
    needs: [generate_study_population]
    outputs:
      moderately_sensitive:
        figure: output/measures/standardised_*.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime:

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

Job information

Status
Failed 
JobRequestError: generate_study_population failed on a previous run and must be re-run
Backend
TPP
Workspace
avoidable-hospitalisations-trends
Requested by
Mark A Green
Branch
main
Force run dependencies
No
Git commit hash
d709985
Requested actions
  • generate_measures
  • process_data

Code comparison

Compare the code used in this Job Request