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Job request: 26856

Organisation:
University of Oxford
Workspace:
maceoutcome
ID:
w5zrk3evnrxgezcp
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:
    generate_dataset
    Status:
    Succeeded
    Job identifier:
    mszbyplmyyi62772
  • Action:
    generate_screening
    Status:
    Succeeded
    Job identifier:
    rmnpleqdypq4zdfd
  • Action:
    audit_dataset
    Status:
    Succeeded
    Job identifier:
    2r7rlsphu45h6qsb
  • Action:
    prepare_cohort
    Status:
    Succeeded
    Job identifier:
    lh4wuvyur2lk6noo
  • Action:
    plot_vaccination_timing
    Status:
    Succeeded
    Job identifier:
    oyubyogffkndwbxo
  • Action:
    describe_cohort
    Status:
    Succeeded
    Job identifier:
    u5szdobg4dscjxdk
  • Action:
    generate_source_activity
    Status:
    Pending
    Job identifier:
    bow2bcihkopzyzsk
    Status message:
    waiting_on_db_workers: Waiting on available database workers
  • Action:
    feasibility_report
    Status:
    Pending
    Job identifier:
    mwdchmbfkyhkmp7d
    Status message:
    waiting_on_dependencies: Waiting on dependencies
  • Action:
    review_feasibility
    Status:
    Pending
    Job identifier:
    e52ekn6jwo2r6xne
    Status message:
    waiting_on_dependencies: Waiting on dependencies

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
      --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

  generate_screening:
    run: ehrql:v1 generate-dataset analysis/screening_dataset.py
      --dummy-tables dummy-tables/small
      --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

  review_feasibility:
    run: r:v2 analysis/review_feasibility.R
    needs: [feasibility_report]
    outputs:
      moderately_sensitive:
        report: output/review/report.html
        tables: output/review/*.csv

Job statistics

Status Count Percentage
Pending 3 33.3%
Running 0 0%
Succeeded 6 66.7%
Failed 0 0%

6 / 9 (66.7%) complete

Timeline

  • Created:

  • Started:

  • Runtime: 00:45:35

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

Job request

Status
Running
Backend
TPP
Workspace
maceoutcome
Requested by
Billy Zhong
Branch
main
Force run dependencies
Yes
Git commit hash
0e85e16
Requested actions
  • run_all

Code comparison

Compare the code used in this job request