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Job request: 26868

Organisation:
University of Oxford
Workspace:
maceoutcome
ID:
s6tl7sabpmldbfxn
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:
    bacr26fidxp2vi2n
  • Action:
    generate_screening
    Status:
    Succeeded
    Job identifier:
    odint3zlpyhksqoh
  • Action:
    prepare_cohort
    Status:
    Succeeded
    Job identifier:
    qk27g7dcfbyysykg
  • Action:
    descriptive_analysis
    Status:
    Succeeded
    Job identifier:
    oy2bxilkxah62cyh
  • Action:
    feasibility_analysis
    Status:
    Succeeded
    Job identifier:
    bvkibyl6ypqth2rh

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

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

  descriptive_analysis:
    run: r:v2 analysis/descriptive_analysis.R
    needs: [prepare_cohort]
    outputs:
      moderately_sensitive:
        baseline: output/descriptive/table1.csv
        vaccination: output/descriptive/vaccination_overlap.csv
        post_fracture: output/descriptive/post_vaccination.csv
        before: output/descriptive/vaccination_before_fracture.png
        after: output/descriptive/vaccination_after_fracture.png
        report: output/descriptive/report.html

  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

  feasibility_analysis:
    run: r:v2 analysis/feasibility_analysis.R
    needs: [prepare_cohort, generate_screening]
    outputs:
      moderately_sensitive:
        report: output/review/report.html
        readiness: output/review/readiness.csv
        flow: output/review/cohort_flow.csv
        monthly: output/review/index_monthly.csv
        definitions: output/review/definition_diagnostics.csv
        sources: output/review/outcome_sources.csv
        timing: output/review/outcome_timing.csv
        followup: output/review/followup.csv
        vaccination: output/review/vaccination_overlap.csv
        post_fracture: output/review/post_vaccination.csv
        missingness: output/review/missingness_by_year.csv
        variables: output/review/variable_review.csv
        observation: output/review/observation_review.csv
        exposure_events: output/review/exposure_events.csv
        baseline_exposure: output/review/baseline_by_exposure.csv
        sequence: output/review/post_vaccine_sequence.csv
      highly_sensitive:
        codes: output/feasibility/gp_record_codes.csv

Job statistics

Status Count Percentage
Pending 0 0%
Running 0 0%
Succeeded 5 100%
Failed 0 0%

5 / 5 (100%) complete

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 02:42:47

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

Job request

Status
Succeeded
Backend
TPP
Workspace
maceoutcome
Requested by
Billy Zhong
Branch
main
Force run dependencies
Yes
Git commit hash
1ca5e95
Requested actions
  • run_all

Code comparison

Compare the code used in this job request