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Job request: 23874

Organisation:
Bennett Institute
Workspace:
wp-work-package-1
ID:
5amxblokuh3djs5z
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Arina Tamborska 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_patient_measures:
    run: ehrql:v1 generate-measures --output output/patient_measures/patient_measures.csv.gz analysis/wp_patient_measures_def.py
    outputs:
      highly_sensitive:
        dataset: output/patient_measures/patient_measures.csv.gz
  generate_practice_measures:
    run: ehrql:v1 generate-measures --output output/practice_measures/practice_measures.csv.gz analysis/wp_practice_measures_def.py
    outputs:
      highly_sensitive:
        dataset: output/practice_measures/practice_measures.csv.gz
  generate_app_measures:
    run: ehrql:v1 generate-measures --output output/appointments/app_measures.csv analysis/appointments/app_measures.py
    outputs:
      moderately_sensitive:
        dataset: output/appointments/app_measures.csv
  generate_app_viz:
    run: r:latest analysis/appointments/app_viz.r
    needs: [generate_app_measures]
    outputs:
      moderately_sensitive:
        app_figures: output/appointments/*.png
  generate_app_summary:
    run: python:latest analysis/appointments/app_summary.py
    needs: [generate_app_measures]
    outputs:
      moderately_sensitive:
        app_table: output/appointments/app_summary.csv
  generate_pre_processing:
    run: python:latest analysis/pre_processing.py 
        --output output/practice_measures/processed_practice_measures.csv.gz
        --output output/patient_measures/processed_patient_measures.csv.gz
        --output output/patient_measures/frequency_table.csv
    needs: [generate_patient_measures, generate_practice_measures]
    outputs:
      highly_sensitive:
        practice_measure: output/practice_measures/processed_practice_measures.csv.gz
        patient_measure: output/patient_measures/processed_patient_measures.csv.gz
      moderately_sensitive:
        frequency_table: output/patient_measures/frequency_table.csv
  generate_measures_viz:
    run: r:latest analysis/viz_measures.r
    needs: [generate_pre_processing]
    outputs:
      moderately_sensitive:
        app_figures: output/*/*.png
        total_measures: output/total_measures/*.csv
  generate_test_data:
    run: ehrql:v1 generate-dataset analysis/dataset.py --output output/patient_measures/test.csv --test-data-file analysis/test_dataset.py
    outputs:
      highly_sensitive:
        dataset: output/patient_measures/test.csv

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 06:00:02

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

Job request

Status
Failed
Backend
TPP
Workspace
wp-work-package-1
Requested by
Arina Tamborska
Branch
main
Force run dependencies
No
Git commit hash
1deae0e
Requested actions
  • generate_patient_measures
  • generate_practice_measures

Code comparison

Compare the code used in this job request