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Job request: 12257

Organisation:
Bennett Institute
Workspace:
with_gp_consultations_curation
ID:
b63njrbwxcgdcrf6
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Jon Massey 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

  • Action:
    generate_measures
    Status:
    Status: Failed
    Job identifier:
    wflxamzucamz6x4n
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_deciles_charts
    Status:
    Status: Failed
    Job identifier:
    6664n2ss25a7wjkk
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_summaries
    Status:
    Status: Failed
    Job identifier:
    23wcxyzyouncydiv
    Error:
    dependency_failed: Not starting as dependency failed
  • Action:
    generate_study_population
    Status:
    Status: Failed
    Job identifier:
    kx355spkhsj6was5
    Error:
    cancelled_by_user: Cancelled by user

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 "2021-01-01 to 2021-12-31 by month"
    outputs:
      highly_sensitive:
        cohort: output/input_*.csv

  generate_measures:
    run: cohortextractor:latest generate_measures
        --study-definition study_definition
    needs: [generate_study_population]
    outputs:
      highly_sensitive:
        measure: output/measure_*.csv

  generate_deciles_charts:
    run: deciles-charts:v0.0.33
        --input-files output/measure_*.csv
        --output-dir output/figures
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        deciles_charts: output/figures/deciles_*_*.*
  
  generate_summaries:
    run: python:latest python analysis/summarise.py
    needs: [generate_measures]
    outputs:
      moderately_sensitive:
        measure_totals: output/tables/measure_*_pivot.csv
        overall_summary: output/tables/overall_summary.csv

Timeline

  • Created:

  • Finished:

  • Runtime:

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

Job request

Status
Failed
Backend
TPP
Workspace
with_gp_consultations_curation
Requested by
Jon Massey
Branch
main
Force run dependencies
No
Git commit hash
04f9915
Requested actions
  • run_all

Code comparison

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