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Job request: 26876

Organisation:
University of Oxford
Workspace:
maceoutcome
ID:
nb7his6jh2d76wgi
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:
    analyse_post_covax
    Status:
    Running
    Job identifier:
    fjdlgy2itvbyp6tm
  • Action:
    analyse_post_fluvax
    Status:
    Running
    Job identifier:
    465yrphmxhzbgi3i
  • Action:
    analyse_pre_covax
    Status:
    Running
    Job identifier:
    63gjwfrhpnwywcey
  • Action:
    analyse_pre_fluvax
    Status:
    Running
    Job identifier:
    qkll25hrspgqq5b5
  • Action:
    manuscript_overview
    Status:
    Succeeded
    Job identifier:
    oqolufiztnfipqcd
  • Action:
    package_manuscript
    Status:
    Pending
    Job identifier:
    6rbvmbnxwl3dnd7j
    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 local synthetic and secure real-data runs.

  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

  manuscript_overview:
    run: r:v2 analysis/manuscript_overview.R
    needs: [prepare_cohort, generate_screening]
    outputs:
      moderately_sensitive:
        tables: output/manuscript/overview/*.csv
        report: output/manuscript/overview/report.html

  analyse_pre_covax:
    run: r:v2 analysis/formal_analysis.R --vaccine covax --design pre --output output/manuscript/pre_covax
    needs: [prepare_cohort]
    outputs:
      moderately_sensitive:
        tables: output/manuscript/pre_covax/*.csv
        trace: output/manuscript/pre_covax/imputation_trace.png
      highly_sensitive:
        imputation: output/manuscript/pre_covax/imputation.rds

  analyse_pre_fluvax:
    run: r:v2 analysis/formal_analysis.R --vaccine fluvax --design pre --output output/manuscript/pre_fluvax
    needs: [prepare_cohort]
    outputs:
      moderately_sensitive:
        tables: output/manuscript/pre_fluvax/*.csv
        trace: output/manuscript/pre_fluvax/imputation_trace.png
      highly_sensitive:
        imputation: output/manuscript/pre_fluvax/imputation.rds

  analyse_post_covax:
    run: r:v2 analysis/formal_analysis.R --vaccine covax --design post --output output/manuscript/post_covax
    needs: [prepare_cohort]
    outputs:
      moderately_sensitive:
        tables: output/manuscript/post_covax/*.csv
        trace: output/manuscript/post_covax/imputation_trace.png
      highly_sensitive:
        imputation: output/manuscript/post_covax/imputation.rds

  analyse_post_fluvax:
    run: r:v2 analysis/formal_analysis.R --vaccine fluvax --design post --output output/manuscript/post_fluvax
    needs: [prepare_cohort]
    outputs:
      moderately_sensitive:
        tables: output/manuscript/post_fluvax/*.csv
        trace: output/manuscript/post_fluvax/imputation_trace.png
      highly_sensitive:
        imputation: output/manuscript/post_fluvax/imputation.rds

  package_manuscript:
    run: r:v2 analysis/package_manuscript.R
    needs: [manuscript_overview, analyse_pre_covax, analyse_pre_fluvax, analyse_post_covax, analyse_post_fluvax]
    outputs:
      moderately_sensitive:
        tables: output/release/*.csv

Job statistics

Status Count Percentage
Pending 1 16.7%
Running 4 66.7%
Succeeded 1 16.7%
Failed 0 0%

1 / 6 (16.7%) complete

Timeline

  • Created:

  • Started:

  • Runtime: 00:01:11

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
No
Git commit hash
d4fa162
Requested actions
  • manuscript_overview
  • analyse_pre_covax
  • analyse_pre_fluvax
  • analyse_post_covax
  • analyse_post_fluvax
  • package_manuscript

Code comparison

Compare the code used in this job request