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Job request: 26855

Organisation:
University of Oxford
Workspace:
maceoutcome
ID:
diie5ylqnnh7qaed
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Billy Zhong 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:
    test_preparation
    Status:
    Succeeded
    Job identifier:
    sgrhjk7a4qmxb4wu
  • Action:
    test_quality_gate
    Status:
    Succeeded
    Job identifier:
    ozzihlysosvcyrsh
  • Action:
    prepare_cohort
    Status:
    Failed
    Job identifier:
    r7d26uuqpeeg2e5p
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_source_activity
    Status:
    Failed
    Job identifier:
    zavdntylxr3n3qxx
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_screening
    Status:
    Failed
    Job identifier:
    beryonpr2j64jq3y
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    plot_vaccination_timing
    Status:
    Failed
    Job identifier:
    zskua3xnk3gwufte
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    generate_dataset
    Status:
    Failed
    Job identifier:
    usjk7dzffid2x3p7
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    audit_dataset
    Status:
    Failed
    Job identifier:
    sjphfs3rx2x5mau2
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    feasibility_report
    Status:
    Failed
    Job identifier:
    ylp3z2go5kfje6ak
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    describe_cohort
    Status:
    Failed
    Job identifier:
    nml7ouz5o5rjbiff
    Status message:
    cancelled_by_user: Cancelled by user
  • Action:
    test_feasibility
    Status:
    Failed
    Job identifier:
    wwfqfqfdsdfzwfzh
    Status message:
    cancelled_by_user: Cancelled by user

Pipeline

Show project.yaml 
version: "5.0"

actions:

# Dummy tables are used locally; the backend supplies real tables in a secure run.
# Keep the same workflow for both. This is a feasibility pipeline, not a final model.

  generate_dataset:
    run: ehrql:v1 generate-dataset analysis/dataset_definition.py
      --dummy-tables dummy-tables/small
      --test-data-file analysis/test_dataset_definition.py
      --output output/dataset.csv
    outputs:
      highly_sensitive:
        dataset: output/dataset.csv


  audit_dataset:
    run: python:v2 python analysis/audit_dataset.py
      --input output/dataset.csv
      --output-dir output/quality
    needs: [generate_dataset]
    outputs:
      highly_sensitive:
        counts: output/quality/feasibility_counts.csv
        checks: output/quality/validation_errors.csv

  prepare_cohort:
    run: r:v2 analysis/prepare_cohort.R
    needs: [generate_dataset, audit_dataset]
    outputs:
      highly_sensitive:
        log: output/logs/prepare_cohort.txt
        dataset: output/analytical_cohort.rds

  describe_cohort:
    run: r:v2 analysis/describe_cohort.R
    needs: [prepare_cohort]
    outputs:
      highly_sensitive:
        baseline: output/tables/table1_feasibility.csv
        vaccination: output/tables/vaccination_by_year.csv
        missingness: output/tables/missingness.csv
        post_fracture: output/tables/post_fracture_vaccination.csv

  plot_vaccination_timing:
    run: r:v2 analysis/plot_vaccination_timing.R
    needs: [prepare_cohort]
    outputs:
      highly_sensitive:
        before: output/figures/vaccination_before_fracture.png
        after: output/figures/vaccination_after_fracture.png

  test_preparation:
    run: r:v2 analysis/test_prepare_cohort.R
    outputs:
      highly_sensitive:
        log: output/logs/test_prepare_cohort.txt

  test_quality_gate:
    run: python:v2 python analysis/test_audit_dataset.py
    outputs:
      highly_sensitive:
        log: output/logs/test_quality_gate.txt

  generate_screening:
    run: ehrql:v1 generate-dataset analysis/screening_dataset.py
      --dummy-tables dummy-tables/small
      --test-data-file analysis/test_screening.py
      --output output/screening.csv
    outputs:
      highly_sensitive:
        dataset: output/screening.csv

  generate_source_activity:
    run: ehrql:v1 generate-measures analysis/source_activity_measures.py
      --dummy-tables dummy-tables/small
      --output output/source_activity.csv
    outputs:
      highly_sensitive:
        measures: output/source_activity.csv

  feasibility_report:
    run: r:v2 analysis/feasibility_report.R
    needs: [prepare_cohort, generate_screening, generate_source_activity]
    outputs:
      highly_sensitive:
        tables: output/feasibility/*.csv
        figure: output/feasibility/source_activity.png

  test_feasibility:
    run: r:v2 analysis/test_feasibility.R
    needs: [prepare_cohort, generate_screening, generate_source_activity]
    outputs:
      highly_sensitive:
        log: output/logs/test_feasibility.txt

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 2 18.2%
Failed 9 81.8%

11 / 11 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:01:44

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

Job request

Status
Failed
Backend
TPP
Workspace
maceoutcome
Requested by
Billy Zhong
Branch
main
Force run dependencies
Yes
Git commit hash
5c135ef
Requested actions
  • run_all

Code comparison

Compare the code used in this job request